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Please Come Back and Degrade This for Me

lacydb1 — Tue, 21 Feb 2023 02:18:36 +0000

Please Come Back and Degrade This for Me lacydb1 Mon, 02/20/2023 - 20:18 RSS:

Georgia C.

When humans engineered synthetic polymers that were virtually impossible to break down, we thought we’d achieved a major victory over the pesky microbes that were shortening the shelf lives of our favorite products. But sometimes winning a fight leads to a whole host of unexpected consequences: in this case, an unmanaged plastic waste crisis threatening the health of humans and the planet we live on. Now, scientists are wondering exactly what it will take to get microbes to come back and degrade what we purposefully designed to be non-biodegradable.

In episode 257 of “This Week in Microbiology” (TWIM), hosts Michael Schmidt, Ph.D., Michele Swanson, Ph.D., and Vincent Racaniello, Ph.D. discussed whether bacterial enzymes might be the solution for the plastic pollution crisis in our oceans. According to the hosts, 9-14 metric tons of plastic enter the oceans every year, adding on to the 150 million metric tons already present there. Plastics in the ocean outnumber sea life by 6:1, and it doesn’t take much searching to find even more disturbing facts about plastic pollution (the Google images results for “ocean plastic gyres” are unforgettable). Why is plastic waste so ubiquitous? Unlike the peptide bonds that form most organic matter, the carbon-carbon bonds that make up synthetic polymers require a high amount of energy to break and are unrecognizable to most microbes¹. However, microorganisms have evolved ways to break down naturally occurring polymers like those in plants – so why not human-made polymers too? This idea was first proposed by Ernest Gale in 1947 – that if there’s carbon in a molecule, some microbe will find a way to utilize it as energy². This idea of “microbial infallibility” has become important for scientists looking for solutions to the plastic problem. The authors of the paper discussed in this episode of TWIM set out to answer one main question: What is the global potential of microbes to degrade plastic?

Although the discovery of plastic-degrading microbes is not new, previous studies used classical techniques: sampling microbes around recycling facilities and testing whatever grew for its ability to degrade plastic³. Although it has been successful in some cases, this approach is inherently low throughput and limits discovery to microbes that can grow in the lab. Zrimec et al. took advantage of recent advancements in global DNA sampling and sequencing for their 2021 study, using hidden Markov models of experimentally verified enzymes to probe for new enzymes capable of degrading plastics⁴. By sampling oceanic and soil populations from around the world, they discovered over 30,000 enzyme sequences with the potential to degrade 10 different types of plastic. They also found a correlation between the amount of potential plastic degrading enzymes and the level of plastic pollution in that region. The TWIM hosts pointed out that this method is not perfect: the authors used the human microbiome to rule out false positives even though microplastics are now so ubiquitous that we consume thousands every day in our diets. However, this paper still serves as a crucial jumping off point for other scientists and engineers to explore the function and manufacturing potential of these enzymes to break down plastic without needing to culture a specific species of bacteria.

So, what will it take to fix the problem of plastic waste? According to the hosts of TWIM, it will take microbiologists, chemical engineers, and synthetic biologists working together to enhance current plastic degradation strategies. But first and foremost, it will require finding microbes willing to make the best out of the mess that humans have created.

References

1. Schmidt, M., Swanson, M., Racaniello, V. I have one word for you: Plastics.

This Week in Microbiology Episode 257. January 2022.

2. Science of Plastics. Science History Institute https://www.sciencehistory.org/science-of-plastics (2016).

3. O’Malley, M. A. & Walsh, D. A. Rethinking microbial infallibility in the metagenomics era. FEMS Microbiol. Ecol. 97, fiab092 (2021).

4. Yoshida, S. et al. A bacterium that degrades and assimilates poly(ethylene terephthalate). Science 351, 1196–1199 (2016).

5. Zrimec, J., Kokina, M., Jonasson, S., Zorrilla, F. & Zelezniak, A. Plastic-Degrading Potential across the Global Microbiome Correlates with Recent Pollution Trends. mBio 12, e02155-21 (2021).

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The Bacterial Assassin and its Tool Kit

lacydb1 — Mon, 20 Feb 2023 00:12:58 +0000

The Bacterial Assassin and its Tool Kit lacydb1 Sun, 02/19/2023 - 18:12 RSS:

Jessica Day

Midway through our journey through the microbial world, Dr. Maria Hadjifrangiskou joined the class on February 3^rd, 2023, to narrate a portion of our tour “Warzone Travel: Bacterial Fight Club.” In this session Dr. Hadjifrangiskou discussed the amazing ability of some bacteria to shoot protein daggers into other cells as a form of attack or defense. This incredible structure is called the type VI secretion system (T6SS).

The T6SS is a highly dynamic nanomachine expressed in Gram negative bacteria, like Vibrio cholera and Pseudomonas aeruginosa. It consists of several proteins that assemble to form a rod-like structure within the bacterium, which is topped with a spike shaped protein called VgrG and subsequently propelled out of the cell by a buildup of intracellular pressure [1]. This structure also contains poisonous cargo that is transferred to the neighboring cell when punctured. These “poison darts” can kill the target cell by preventing cell division, disrupting the lipid bilayer, compromising protein production, and more. Contact between bacteria is often necessary for an effective attack with the T6SS, as the protein cannot be shot with enough force to cross larger distances. In addition, this contact is even used as an indicator to start an attack against an enemy bacterium that might slip past the defenses.

While the T6SS is an important tool for bacterial assassins, some are better trained than others and you might even say some have a strong sense of justice. V. cholera is a Gram-negative bacteria known to cause cholera in humans, but its use of the T6SS is not highly regulated [2]. The V. cholerae that express the T6SS abuse the power of the system, attacking at random and with voracity. Another Gram-negative bacterium, P. aeruginosa, is highly specific in its targets, raising a counterattack only when directly threatened [3]. Studies from the Mekalanos lab characterized the differences in how these two bacterial species use the T6SS to their advantage. When comparing P. aeruginosa attacks to V. cholera attacks, they observed that P. aeruginosa only attacked V. cholera when it was actively deploying its T6SS. P. aeruginosa did not attack V. cholera with non-functional T6SS, instead living peacefully in the heterogeneous mixture [3]. These interactions could be highly important for mediating communication between different types of bacteria in communities.

Despite the somewhat unsettling idea of bacteria having assassin-like tools, the T6SS is an extremely interesting area of investigation. It appears to be important not only in competition, but also in communication and maintenance of biofilms. Most organisms within a given community have genes that encode the T6SS, yet only 10-12% express the system, raising the question of how it is decided which bacteria will rise to the front lines and fight for their territory. There are still many questions to be explored in this field to learn more about how bacteria can fight each other, other species of bacteria, and even host cells.

References

Coulthurst, S. (2019). The Type VI secretion system: a versatile bacterial weapon. Microbiology, 165(5), 503-515.
Crisan, C. V., & Hammer, B. K. (2020). The Vibrio cholerae type VI secretion system: toxins, regulators and consequences. Environmental Microbiology, 22(10), 4112-4122.
Basler, M., Ho, B.T., and Mekalanos, J.J. (2013) Tit-for-tat: type VI secretion system counterattack during bacterial cell-cell interactions. Cell 152: 884–894.

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Fleaing the Plague

lacydb1 — Mon, 13 Feb 2023 00:12:18 +0000

Fleaing the Plague lacydb1 Sun, 02/12/2023 - 18:12 RSS:

Emma Peacock

Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt hosted episode 255 of the podcast “This Week in Microbiology” entitled "Fleaing the Plague.” During the episode, they discussed two papers published in late 2021. The first paper by Kehe et al. focused on positive interactions within microbial communities under varying carbon conditions. Previously, positive interactions between microbes were thought to be rare, having been observed in less than 10% of cases in a previous study². However, using a kChip to measure interactions between co-cultures of soil bacteria in different carbon conditions where each co-culture consisted of two different bacterial species, one fluorescently labeled and one unlabeled, Kehe et al. discovered that positive interactions accounted for almost half of all interactions. They also found that these interactions were especially frequent between taxonomically and metabolically diverse strains.

Personally, I found the authors’ use of the term “positive interaction” to be a bit misleading, initially thinking that these interactions were mutually beneficial to multiple bacterial strains within a community. However, the authors defined an interaction as positive if growth yield increased only for the labeled bacterial species within a co-culture instead of both the labeled and unlabeled species present. Applying this definition, the authors identified half of the observed positive interactions to be parasitic with a small percentage of commensalistic relationships and an even smaller percentage of mutualistic relationships making up the rest of the positive interactions. Though the classification of interactions was counterintuitive, the study did illustrate the importance of diversity within microbial communities and microbial ecology, which has since led to studies expanding on these interactions such as viral pathogenicity during co-infection³.

The second paper discussed was a study by Bland et al. on the yersinia murine toxin found in Yersinia pestis, the bacteria responsible for plague. While the plague is commonly thought to be a thing of the past, new cases of plague are still reported every year, often contracted through flea bites⁵. Surprisingly, Y. pestis is a fairly young pathogen, originating less than 6,000 years ago with very few genetic differences from its ancestral bacteria that allowed it to be transmittable by fleas. One such difference was the addition of the yersinia murine toxin (Ymt) gene which increases the survival of Y. pestis when infected blood is taken up by fleas, but only if the blood originated from certain species of mammals, like black rats (R. rattus) as opposed to brown rats (R. norvegicus)⁴. Bland et al. discovered that the blood biochemistry of some mammals impacted the survival of Y. pestis without the Ymt gene in the flea gut. They determined that Ymt was essential for Y. pestis survival and transmission in fleas as it protects against an antibacterial agent present during flea digestion. This study provided insight into the role of Ymt in the persistence of Y. pestis and the evolutionary and ecological history of “flea-borne plague”⁴.

Overall, while the two papers appeared to be on very different topics, they both shared a common theme. Both studies highlighted the importance of evolutionary and ecological relationships microbes have developed with each other and with other species. I feel that a deep understanding of these relationships will play a significant role in future studies, particularly those regarding microbiomes, anti-microbial resistance, and viral transmission.

References

Kehe, J., Ortiz, A., Kulesa, A., Gore, J., Blainey, P. C., & Friedman, J. (2021). Positive interactions are common among culturable bacteria. Science Advances, 7(45), eabi7159. https://doi.org/10.1126/sciadv.abi7159
Foster, K. R., & Bell, T. (2012). Competition, not cooperation, dominates interactions among culturable microbial species. Current Biology: CB, 22(19), 1845–1850. https://doi.org/10.1016/j.cub.2012.08.005
Shirley, K., & Loftis, J. M. (2022). A spotlight on HCV and SARS-CoV-2 co-infection and brain function. Pharmacology, Biochemistry, and Behavior, 217, 173403. https://doi.org/10.1016/j.pbb.2022.173403
Bland, D. M., Miarinjara, A., Bosio, C. F., Calarco, J., & Hinnebusch, B. J. (2021). Acquisition of yersinia murine toxin enabled Yersinia pestis to expand the range of mammalian hosts that sustain flea-borne plague. PLoS Pathogens, 17(10), e1009995. https://doi.org/10.1371/journal.ppat.1009995
CDC. (2022, November 16). Plague surveillance | CDC. Centers for Disease Control and Prevention. https://www.cdc.gov/plague/maps/index.html

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Staphylococcus aureus & Candida albicans Polymicrobial Infection Makes Virulence A Bigger Problem

lacydb1 — Mon, 06 Feb 2023 22:28:26 +0000

Staphylococcus aureus & Candida albicans Polymicrobial Infection Makes Virulence A Bigger Problem lacydb1 Mon, 02/06/2023 - 16:28 RSS:

Alex Blatt

Todd OA, Fidel PL Jr, Harro JM, Hilliard JJ, Tkaczyk C, Sellman BR, Noverr MC, Peters BM. Candida albicans Augments Staphylococcus aureus Virulence by Engaging the Staphylococcal agr Quorum Sensing System. mBio. 2019 Jun 4;10(3):e00910-19. doi: 10.1128/mBio.00910-19. PMID: 31164467; PMCID: PMC6550526.

Todd et al.’s research describes how Candida albicans augments Staphylococcus aureus virulence by the engagement of S. aureus’s accessory gene regulator (agr) quorum sensing system. Quorum sensing is a density-dependent communicative signaling system that regulates coordinated gene expression within a population.¹ In bacteria such as S. aureus, the quorum sensing system relies on the accumulation of a signaling molecule that is produced, recognized, and only at certain concentrations, can modulate gene expression. The authors discovered that the agr virulence factor production, such as alpha-toxins, were increased and driven by the modulation of extracellular increase in pH (alkalinization) in co-culture with Candida in vitro. This is an eye-opening revelation of how a coinfection from these two pathogens can proliferate lethal synergism towards the host.²S. aureus, which is a Gram-positive bacterium, contains an agr quorum-sensing system that senses the local concentrations of cyclic peptide signaling molecules (autoinducing peptides) as its own population density increases to stimulate specific gene expression patterns.³ The study utilized a murine intrabdominal infection (IAI) model and an S. aureus GFP reporter to reveal agr quorum sensing system activation in monomicrobial and polymicrobial in vivo and in vitro growth.² The significance of this study is that very little was known about the complex “cross talk” interaction between microbes that change signaling pathways and shape health and diseases within humans and other species.

The study illustrated the synergistic virulence of C. albicans and S. aureus in mice, where intraperitoneal co-culture injection resulted in morbidity symptoms, such as hunching and slow reaction, around 12 hours post-inoculation.² After one day, there was around a 10% survival rate of the co-infected mice and above a 95% survival rate in the mono-cultured mice who went on to survive up to ten days.² This was fascinating, yet terrifying, to see how drastic lethal coinfections were compared to the mono-infections in mice. The authors found an increased expression of agr toxin production with the presence of C. albicans by qPCR in Figure 3², which wasn’t due to normal growth in measuring the colony forming units (CFUs)/mL clarified in Figure 2.² The hemolytic activity was also tested to measure red blood cell lysis suggesting a greater hemolytic toxin production observed from co-culture compared to the mono-cultures in Figure 4.

Although the study pointed out the increase in alpha-toxin production, the question remained whether alpha-toxin production alone effected the survival rate and significantly drove lethal synergistic IAIs in mice. The authors concluded in Figure 6 that alpha-toxin was necessary in driving infection, but insufficient in driving lethality during co-infection.² Perhaps the production of other S. aureus toxins or the heterogeneity of C. albicans strains could be the necessary contributing factor towards driving lethality during co-infection. It remains unclear whether or not the enhancement of agr alpha-toxin production is shared amongst all C. albicans strains to various degrees and responses. Lastly, insight into the bacterial-fungal quorum sensing cross-talk in the agr pathway could further the progress of developing therapies needed for reducing the severity of illness in patients with these co-infections.

References:

Miller MB, Bassler BL. Quorum sensing in bacteria. Annu Rev Microbiol. 2001;55:165-99. doi: 10.1146/annurev.micro.55.1.165. PMID: 11544353.
Todd OA, Fidel PL Jr, Harro JM, Hilliard JJ, Tkaczyk C, Sellman BR, Noverr MC, Peters BM. Candida albicans Augments Staphylococcus aureus Virulence by Engaging the Staphylococcal agr Quorum Sensing System. mBio. 2019 Jun 4;10(3):e00910-19. doi: 10.1128/mBio.00910-19. PMID: 31164467; PMCID: PMC6550526.
Jenul C, Horswill AR. Regulation of Staphylococcus aureus Virulence. Microbiol Spectr. 2019 Apr 5;7(2):10.1128/microbiolspec.GPP3-0031-2018. doi: 10.1128/microbiolspec.GPP3-0031-2018. PMID: 30953424; PMCID: PMC6452892.

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Lavender and Catheters

lacydb1 — Mon, 06 Feb 2023 01:50:52 +0000

Lavender and Catheters lacydb1 Sun, 02/05/2023 - 19:50 RSS:

Erykah Coe

In Episode 263 of the This Week in Microbiology Podcast, the hosts discussed the recent findings of two 2022 papers. The manuscripts are entitled: The elimination effects of lavender essential oil on Listeria monocytogenes biofilms developed at different temperatures and the induction of VBNC state (Han et al.) and Inhibiting host-protein deposition on urinary catheters reduces associated urinary tract infections (Andersen et al.).

Han et al. investigated the effects of lavender essential oil on biofilm formation of Listeria monocytogenes, a foodborne pathogen that can enter a non-culturable state. The researchers evaluated the elimination effects of four common antimicrobial agents, lavender oil, lactic acid, sodium hypochlorite and hydrogen peroxide, on mature biofilms of L. monocytogenes at different temperatures, 10°C (cold biofilms) and 32°C (warm biofilms). The results showed that lavender oil and sodium hypochlorite (75%) were the best agents for disrupting the biofilms, with lavender oil being able to remove up to 83% of the biofilm at four times the minimum inhibitory concentration. The authors focused on lavender oil due to past literature documenting the oil’s effect on Staphylococcus aureus² and Campylobacter jejuni³. The authors were also interested in understanding the effects of lavender oil on mature biofilms at the different biofilm temperatures? mentioned earlier. The study also discovered that lavender oil was more efficient in lowering the number of viable cells, and that biofilms created at 10 °C were less vulnerable to the sanitizers than those formed at 32°C. Overall, among the evaluated antimicrobial agents, lavender oil was found to have the most significant eradication impact on Listeria biofilms.

Andersen et al. conducted a study to examine the inhibition of host-protein fibrinogen deposition and biofilm formation on catheters in a mouse model. They looked at different catheter materials coated with liquid-infused silicon (LIS) and soaked in medical-grade silicon oil. The study determined that LIS inhibits fibrinogen binding to a range of different UTI-causing pathogens, such as uropathogenic E. coli (UPEC) and Pseudomonas aeruginosa. The researchers used an in vitro model to show that fibrinogen promotes the initial binding of uropathogens to LIS catheters and found that colonization of LIS catheters was significantly reduced. They also demonstrated that LIS modification successfully reduced the fibrinogen-microbial binding platform and disrupted uropathogen biofilm formation on catheters and colonization of the bladder in vivo. The study suggests that disrupting the uropathogen-fibrinogen interaction can reduce the ability ofpathogens to bind and colonize on the catheter surface and bladder.

In the Han et al. paper, the authors did not explore the effects of lactic acid and hydrogen peroxide on metabolic activity, viable and culturable cells, and the observation via confocal laser scanning microscopy of the cold and warm biofilms. Also, the potential for antimicrobial resistance of lavender oil as a treatment for L. monocytogenes infections was not discussed. In the discussion about the Andersen et al. paper, one of the hosts, Dr. Petra Levin mentioned that E. coli exhibits a pilus adhesion protein called FimH that can potentially bind to fibrinogen. During my first rotation, I worked with UPEC to understand if different carbon sources alter the morphology of UPEC colony biofilms. It would be interesting to see how the LIS catheter will manage bacteria that are grown in different sugars and concentrations, like mannose, which can inhibit bacteria by interacting with the E. coli type 1 pilus adhesion protein, FimH. I concluded that mannose alters the rugosity and genetically manipulates UTI89 and VUTI137 when introduced into the sugar environment. Therefore, I suggest that introducing sugar fed UPEC isolates into the murine bladder could make it harder to get rid of the adhesion properties of FimH and the uropathogen. It would be interesting to see how the LIS catheter would work in this scenario.

Cited Articles

Han, X., Chen, Q., Zhang, X., Peng, J., Zhang, M., & Zhong, Q. (2022). The elimination effects of lavender essential oil on Listeria monocytogenes biofilms developed at different temperatures and the induction of VBNC state. Letters in applied microbiology, 74(6), 1016–1026. https://doi.org/10.1111/lam.13681
Brożyna, M., Paleczny, J., Kozłowska, W., Chodaczek, G., Dudek‐Wicher, R., Felińczak, A., Gołębiewska, J., Górniak, A. and et al. (2021) The antimicrobial and antibiofilm in vitro activity of liquid and vapour phases of selected essential oils against Staphylococcus aureus. Pathogens 10, 1207–1232.
Ramić, D., Bucar, F., Kunej, U., Dogša, I., Klančnik, A. and Možina, S.S. (2021) Antibiofilm Potential of Preparations against Campylobacter jejuni. Appl Environ Microbiol 87, 1099–1021.
Marissa Jeme Andersen, ChunKi Fong, Alyssa Ann La Bella, Jonathan Jesus Molina, Alex Molesan, Matthew M Champion, Caitlin Howell, Ana L Flores-Mireles (2022) Inhibiting host-protein deposition on urinary catheters reduces associated urinary tract infections eLife 11:e75798. https://doi.org/10.7554/eLife.75798

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Broadening the Microbiome: Fungi in Inflammatory Bowel Diseases (IBD)

lacydb1 — Mon, 07 Mar 2022 14:51:30 +0000

Broadening the Microbiome: Fungi in Inflammatory Bowel Diseases (IBD) lacydb1 Mon, 03/07/2022 - 08:51 RSS:

Tina C.

https://asm.org/Articles/2021/July/Broadening-the-Microbiome-Fungi-in-Inflammatory-Bo

I recently read a blog post by Christy Clutter that discusses the role of fungi in Inflammatory bowel disease (IBD). IBD is characterized by immune hyperactivation that damages the intestine of about 3 million Americans, and includes Crohn’s disease and ulcerative colitis. Although 240 genetic variations associated with increased likelihood of IBD development have been identified, epidemiological studies show that strong environmental factors such as diet, antibiotic exposure, and smoking can affect individual susceptibility. Inappropriate immune responses to the microbes existing in the intestine could result in the development of IBD; therefore, it is important to understand how these environmental factors drive disease susceptibility in the gut microbiome.

Most microbiome research is focused on bacterial populations because they make up trillions of organisms, but bacteria are not the only microbes that inhabit the gut. Less than 1% of microbiota studies have included fungi which leaves current knowledge of microbiomes under characterized. Although most gut microbes are bacteria, fungi have been implicated in causal roles for gut microbial ecology and host immune functionality in mice (Bernardes, et al. 2020). Current sequencing tools for fungi and bacteria are similar, but there is a lack of diversity in the species identified due to sampling, and data analyses methods are biased to a small set of over-represented species. The author states that fungal reference databases used to identify sequences are "fledgling", and that bioinformatic ability to trust these taxonomic identifications is imperfect. I would argue that current databases of fungi sequencing data are suitable for trustworthy phylogenetic and taxonomic identifications. The National Center for Biotechnology Institute has a plethora of fungi sequence data that is updated daily, most notably to mycologists is the Fungal RefSeq database that includes more than 200 species (Robbertse & Tatusova 2011). Most fungi identified in the clinical laboratories are yeast, and all 1,200 known species of yeast have now been sequenced by the Y1000+ Project (Shen, et al. 2018). The Y1000+ Project has sequenced the highest number of fungal species thus far, and the final version of the publicly available database will include all yeast fungal species (https://y1000plus.wei.wisc.edu/).

Scientists studying IBD have taken interest in fungi because like bacteria, they are ubiquitous in the body, and are sensitive to environmental factors such as diet. Patients with Crohn's disease have elevated circulating antifungal antibodies, and some species such as Candida albicans actively worsen inflammatory colitis in mice (Jawhara, et al. 2008). Fungi influence bacterial dynamics in the gut by acting in cooperation with host infection and biofilm production. For example, Candida tropicals can work with bacteria such as Escherichia coli and Serratia marcescens to generate a "monstrous biofilm", as well as induce the expression of fungal markers for pathogenicity (Hoarau, et al. 2016). Recent studies have shown that there is dysbiosis not only with bacterial species but also fungal species in patients with IBD. There exists inherent competition between fungi and bacteria within the gut, which means that antibiotics used to treat intestinal disease can disrupt more than just bacterial communities. Antibiotics selectively eliminate specific bacteria while leaving fungal species undisturbed, thus they can change the dysbiosis in the gut microbiome resulting in higher prominence of fungal species. Even though there is much research on the gut microbiome, little is still known about the diversity of its key microbial players. Databases such as Fungal RefSeq and Y1000+ could be a great resource in the development of specialized methods for identifying which fungal species contribute to the gut microbiome of patients with IBDs.

References

Bernardes E., Pettersen V.K., Gutierrez M.W., Laforest-Lapointe I., Jendzjowsky N.G., Cavin J.B., Vicentini F.A., Keenan C.M., Ramay H.R., Samara J., MacNaughton W.K., Wilson R.A., Kelly M.M., McCoy K.D., Sharkey K.A., Arrieta M.C. (2020). Intestinal fungi are causally implicated in microbiome assembly and immune development in mice. Nat Commun. 11(1):2577. doi: 10.1038/s41467-020-16431-1.

Hoarau, G., Mukherjee, P.K., Gower-Rousseau, C., Hager, C., Chandra, J., Retuerto, M.A., Neut, C., Vermeire, S., Clemente, J., Colombel, J.F., Fujioka, H., Poulain, D., Sendid, B., Ghannoum, M.A (2016). Bacteriome and Mycobiome Interactions Underscore Microbial Dysbiosis in Familial Crohn's Disease. mBio, 7(5):e01250-16. https://doi.org/10.1128/mBio.01250-16

Jawhara, S., Thuru, X., Standaert-Vitse, A., Jouault, T., Mordon, S., Sendid, B., Desreumaux, P., Poulain, D. (2008). Colonization of Mice by Candida albicans Is Promoted by Chemically Induced Colitis and Augments Inflammatory Responses through Galectin-3, The Journal of Infectious Diseases, 197(7), 972–980. https://doi.org/10.1086/528990

Robbertse, B., & Tatusova, T. (2011). Fungal genome resources at NCBI. Mycology, 2(3), 142–160. https://doi.org/10.1080/21501203.2011.584576

Shen, X.X., Opulente, D.A., Kominek, J., Zhou, X., Steenwyk, J.L., Buh, K.V., Haase, M.A.B., Wisecaver, J.H., Wang, M., Doering, D.T., Boudouris, J.T., Schneider, R.M., Langdon, Q.K., Ohkuma, M., Endoh, R., Takashima, M., Manabe, R.I., Cadez, N., Libkind, D., Rosa, C.A., DeVirgilio, J., Hulfachor, A.B., Groenewald, M., Kurtzman, C.P., Hittinger, C.T., Rokas, A. (2018). Tempo and mode of genome evolution in the budding yeast subphylum. Cell 175: 1533-45. https://doi.org/10.1016/j.cell.2018.10.023

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Evolution of a Protective Symbiont in Honey Bees by Professor Irene Newton, PhD

lacydb1 — Thu, 03 Mar 2022 19:01:58 +0000

Evolution of a Protective Symbiont in Honey Bees by Professor Irene Newton, PhD lacydb1 Thu, 03/03/2022 - 13:01 RSS:

Monique Porter

Speaker Background: Dr. Irene Newton, PhD, specializes in mechanisms of symbiosis; specifically, the molecular mechanisms of host-microbe symbiotic interactions. She obtained her PhD from Harvard University and conducted postdoctoral research at Tufts University. She is currently an associate professor at Indiana University.

Seminar Summary: Apis mellifera, the western honey bee, develop from egg to pupae within their colony. Throughout the development, they come into contact with different microbiota (Gilliamella, Snodgrassella, Bombella, Lactobacillus) through nectar, pollen, and interaction with other bees. These interactions can establish the gut microbiota, help protect against potential pathogens, and aid in nutrient acquisition. Using honey bees as models, Newton aimed to study how society, genetics, and behavior affect the microbial community.

First, Newton examined the queen microbiome during and after development. She sampled both queens and workers at various time points of development to determine the microbiota and if the queens and workers microbiota were similar, indicating microbial exchange. In her findings, Newton explained that the worker and queen microbiota are distinct, and do not share microbial composition. The queens were also variable in the microbial composition and titer.

Community composition of the workers contain the “core” microbes. However, the queens had a larger composition of microbes, especially Bombella. Bombella is often referred to as the queen microbiota since it is not found commonly in the worker digestive tract. Newton attributed the differences in microbiota in queens vs. workers to physiological differences, since queens have larger ovaries and live for years, while workers typically live for 3-4 weeks. Also, queens are fed royal jelly, a specific diet that rears queen bees. Newton hypothesized that the royal jelly is pre-inoculated with Bombella apis, developing a distinct queen microbiota.

Next, Newton aimed to better understand the origin of B. apis, and its relationship with royal jelly. Through phylogenetic analysis, her team determined that B. apis is closely related to Saccharibacter, a flower-associated organism. Through sequence composition, synteny, phylogenetic methods, and functional analysis, she questioned if there were horizontally transferred regions between flower-associated Saccharibacter and B. apis. Results revealed that HGT1 is conserved across B. apis honeybee strains, and its function is currently unknown. HGT4 and HGT5 are also conserved and are metabolic gene regions that aid in immune defenses and the metabolism of sugars. Overall, B.apis acquired multiple metabolic and defense gene regions that protect the honey bee from other pathogens, and these genes contain signatures of honey bee association as they are distinct from Saccharibacter, a flower-associated organism.

Personal Review: I found Dr. Newton’s presentation very interesting and impactful. I broadly have experience with bumble bee microbiota, but honey bees are very different, and so is their microbiota. As Dr. Newton mentioned in her presentation, microbiome research is almost exclusive to workers and not queens. Even in bumble bee research, studies exhaustively use workers, but queen health homeostasis is much less understood. Dr. Newton was not only able to include queen microbiota samples, but additionally, relate and compare it back to workers. This study is very impactful to the field and combining the wet lab data collection and the dry lab data analysis is impressive, and it makes me excited to find out what her team is doing next. Dr. Irene Newton is a scientist I would love to connect with in the future, and I am fortunate to hear about her research through the Vanderbilt Microbiome Innovation Center.

Note: Seminar was presented on Wednesday, October 14^th, 2020, and was viewed on
Vanderbilt Microbiome Innovation Center channel on YouTube.

https://www.youtube.com/watch?v=nBDIjsgSzZ4&t=601s

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Can Gut Microbes Cause Cancer?

lacydb1 — Wed, 02 Mar 2022 14:06:36 +0000

Can Gut Microbes Cause Cancer? lacydb1 Wed, 03/02/2022 - 08:06 RSS:

Amelia Cephas

The Western-style diet is chock full of high fat, processed and refined foods that often cause systemic damage to the human body. One particular effect that high fat foods have on the body involves the microbes in the gastrointestinal tract. Many studies have shown the association between the colonization of a subset of microbes in the gut and colorectal and gastric cancer onset. The question of interest is: can what we eat really lead to the onset of gastrointestinal cancer?

Interestingly, diet directly affects the types of bacteria that typically colonize the gut. Though both extrinsic (e.g., diet, medications) and intrinsic factors (genetics, metabolic regulation, etc.) determine the bacterial composition within the gut, the former has the most predominant effect (1). For instance, fiber-rich foods such as nuts, legumes, grains, vegetables and fruit are associated with the growth of Bifidobacterium, Lactobacillus and lactic acid bacteria. These foods, also known as prebiotics, lead to the production of butyrate, acetate, propionate and short chain fatty acids by obligate anaerobes such as those in the Firmicutes and Bacteroidetes phyla (1). On the other hand, the consumption of high fat foods leads to the increase in facultative anaerobes in the gut such as Enterobacteriaceae, which are abundant in the feces of individuals on high fat diets (2). Thus, a healthy intestinal environment has a hypoxic colonic surface, generally, while an unhealthy gut contains more terminal electron receptors such as oxygen and nitrate in the colonic epithelia, which facultative anaerobes use to survive in the gut (2). Ultimately, it’s safe to say the cliché: “you are what you eat”, as the microbes in your gut will tell a great deal about what you generally consume.

So, what is the link between these microbes and cancer? The answer is not so simple, but a recent Science paper might hold some insight. In this paper, researchers sought to determine how diet-induced changes in intestinal physiology alter the metabolic capacity of the microbiota. Using a high-fat and low-fat feeding model, they showed that high-fat diet fed mice had gut epithelial metaplasia, increased abundance of [1], mucosal inflammation, reduced mitochondrial activity, reduced hypoxia, and that a prolonged high-fat diet escalates Escherichia coli choline metabolism (3). Interestingly, several species of E.coli (e.g pks+) and other Enterobacteria are detected more frequently in patients with colorectal cancer (CRC) compared to healthy individuals. These genotoxic metabolites, which damage DNA and are found to induce mutation in genes (e.g Adenomatous polyposis coli-APC) (2, 4). Mutations that disrupt APC signaling pathways are found in 80% of CRC patients. The fact that approximately 65% of CRC cases are sporadic, and environmental factors such as diet are likely to play a major role in its onset should be a warning to individuals who tend to ignore their nutritionists and doctors!

References:

Leeming ER, Johnson AJ, Spector TD, Le Roy CI. Effect of Diet on the Gut Microbiota: Rethinking Intervention Duration. Nutrients. 2019 Nov 22;11(12):2862. doi: 10.3390/nu11122862
Foegeding NJ, Jones ZS, Byndloss MX. Western lifestyle as a driver of dysbiosis in colorectal cancer. Dis Model Mech. 2021 May 1;14(5): doi: 10.1242/dmm.049051.
Yoo W, Zieba JK, Foegeding NJ, Torres TP, Shelton CD, Shealy NG, Byndloss AJ, Cevallos SA, Gertz E, Tiffany CR, Thomas JD, Litvak Y, Nguyen H, Olsan EE, Bennett BJ, Rathmell JC, Major AS, Bäumler AJ, Byndloss MX. High-fat diet-induced colonocyte dysfunction escalates microbiota-derived trimethylamine N-oxide. Science. 2021 Aug 13;373(6556):813-818. doi: 10.1126/science.aba3683.
Dougherty MW, Jobin C. Shining a Light on Colibactin Biology. Toxins (Basel). 2021 May 12;13(5):346. doi: 10.3390/toxins13050346.

[1] High fat foods are rich in choline, which is catabolized by gut microbes

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Journey into a mosquito

lacydb1 — Tue, 01 Mar 2022 18:35:03 +0000

Journey into a mosquito lacydb1 Tue, 03/01/2022 - 12:35 RSS:

Chiamaka D. Okoye

Mosquitoes beat humans as the world’s deadliest animals.¹ This is not because they directly kill people, but instead they are really good at being vectors, which are organisms that act as vehicles for pathogens to transfer between hosts. Mosquitoes are notorious for transmitting viruses like yellow fever and dengue, bacteria that cause Lyme disease and typhus, protozoans that cause malaria, and metazoans that cause lymphatic filariasis, to name a few. These pathogens are often acquired by the mosquito via horizontal transmission through an intermediate host. The ability of the mosquito to acquire and transmit pathogens to susceptible hosts, or its ‘vector competence,’ is influenced by numerous internal factors like its preference for host, time taken for the pathogen to develop within the host, and the microbiome, as well as external factors like temperature and predator density.²

Malaria is one of the most devastating diseases transmitted by mosquitoes. This disease is endemic in over 100 countries with a tropical climate, infecting about 229 million people as of 2020 and causing about 409,000 deaths annually, mostly in children.³ Symptoms of the disease may include fever, chills, vomiting, exhaustion, anemia, and organ failure. The Plasmodium parasites are the causative agents of malaria in humans. Plasmodium falls under the Apicomplexa phylum which consist of parasitic, unicellular eukaryotes that use an apical complex to invade a host cell during part of their lifecycle. For Plasmodium, its lifecycle involves two hosts – mosquitoes and humans. In the mosquito, the parasite undergoes sexual reproduction; the macro and micro gametocytes ingested during a blood meal encounter each other in the mosquito’s gut to form oocytes, which progress to form several thousand copies of sporozoites. When a mosquito encounters a human host, it delivers the sporozoites along with its saliva. The sporozoites migrate to the liver where they are amplified and progress to form merozoites that can infect red blood cells. The merozoites replicate to produce about 30 more copies each, before lysing the red blood cells, which causes anemia, and going on to replenish gametocytes that get ingested by mosquitoes to propagate the cycle.²

Considering that we would be saving many lives each year by eradicating mosquitoes, why don’t we just kill them off? The truth is that not all mosquitoes are bad; there are about 3,500 species of which only the blood-sucking females of 100 species are vectors for parasites. Most mosquitoes feed off plant-based sources and serve as food for birds, fish, and other animals in the ecosystem.⁴ Hence, killing them off would most likely come with negative environmental consequences. Alternative approaches have turned to making mosquitoes resistant to the parasites they transmit.⁴ For example, the Australian-based World Mosquito Program breeds mosquitoes that carry Wolbachia bacteria to prevent the spread of viruses like dengue, Zika, yellow fever and chikungunya.⁵Wolbachia is proposed to function by activating host immunity in mosquitoes or by competing for cellular resources with the RNA viruses they transmit.⁶ Other groups are looking to genetically modify mosquitoes to prevent parasitic transmission.⁷

References

1. Gates, B. The deadliest animal in the world. https://www.gatesnotes.com/health/most-lethal-animal-mosquito-week.

2. Hillyer, J., IGP 8002 - Adventure guide to the microbial world: Journey into a mosquito. 2022.

3. World malaria report 2020; Global Malaria Programme, 30 November, 2020.

4. Bates, C., Would it be wrong to eradicate mosquitoes? 28 January, 2016.

5. World Mosquito Program. https://www.worldmosquitoprogram.org/en/work/about-us.

6. Pimentel, A. C.; Cesar, C. S.; Martins, M.; Cogni, R., The Antiviral Effects of the Symbiont Bacteria Wolbachia in Insects. Frontiers in Immunology 2021, 11.

7. Pike, A.; Dong, Y.; Dizaji, N. B.; Gacita, A.; Mongodin, E. F.; Dimopoulos, G., Changes in the microbiota cause genetically modified Anopheles to spread in a population. Science 2017, 357 (6358), 1396-1399.

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A Tick's Meal

lacydb1 — Thu, 24 Feb 2022 20:21:16 +0000

A Tick's Meal lacydb1 Thu, 02/24/2022 - 14:21 RSS:

Kacie Traina

On episode 258 of the podcast “This Week in Microbiology”, Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt discussed two main topics focused on anti-genetic variation within dengue virus serotypes and how a novel mRNA vaccine could induce antibodies against tick proteins to prevent transmission of Lyme disease. The first portion of the episode discussed dengue, which is a single-stranded, enveloped RNA virus that causes over 50 million known cases per year. There are four different serotypes, or distinct variations, of dengue that lead to infection in humans. With the rate of infection and different serotypes, understanding more about the immunology of dengue and especially the variation between these serotypes is very important.

One of the main topics discussed was whether antigenic variation made the dengue virus more fit. To assess if there was a fitness advantage with the dengue serotypes, studies looked at the pattern of serotypes from over 8,000 infections during outbreaks in Southeast Asia from 1970 to 2015. It was concluded that antigenic fitness is a major driver of dengue infection population genetics from year to year. Recovery from dengue infection is believed to provide lifelong immunity against that specific serotype. However, cross-immunity, the protection against a given pathogen resulting from immunity acquired from past exposure to a related pathogen or its antigens, of one dengue serotype to the other serotypes after recovery is only partial and temporary. Subsequent infections by other serotypes increase the risk of developing more severe dengue. Research showed that protection against a dengue serotype dropped 63% each year for the first two years following a dengue infection. I think understanding more about the serotypes and population genetics as performed in this study could be greatly beneficial in further development of treatments or a vaccine against dengue. Similar to the mutating variants of SARS-CoV-2 and the various influenza strains we encounter each year, understanding and being able to predict prominent serotypes of dengue could help reduce the rate of infections.

The second story in this episode of “This Week in Microbiology” focused on the creation of an mRNA vaccine that induces antibodies against tick proteins and prevents the transmission of Lyme disease, as described in a recent publication (Sajid, A. et al). Black-legged ticks transmit the bacteria Borrelia burgdorferi, which causes Lyme disease. The authors of the paper aimed to develop a new tool to prevent the spread of Lyme disease: a vaccine that stops ticks from feeding properly once they latch onto a host’s skin, which stops them from transmitting B. burgdorferi. Guinea pigs can develop a natural resistance to tick bites after being repeatedly bitten. At the tick bite sites, guinea pigs develop an inflamed, red welt and the immune reaction interferes with the tick’s ability to continue drinking the blood of its host. Evidence suggests that humans can also build up similar resistance to ticks. Building off of this idea of tick immunity, researchers sought to develop a vaccine to help humans become better protected from tick-borne pathogens like B. burgdorferi.

When a tick feeds, it takes time for the bacteria to be transmitted so the tick must remain attached for 36-48 hours. The tick’s spit helps it avoid discovery during feeding because the saliva contains proteins that suppress the host’s immune response, which reduces the amount of pain and inflammation triggered by the bite. The authors developed an mRNA vaccine using a complex blend of 19 different tick salivary proteins to help provide host protection specifically against those proteins. The goal of the vaccine was to give the host the chance to see these antigens first, before being bitten, in order to develop immunity. To test the vaccine, guinea pigs were immunized and their blood was tested for antibodies against the salivary proteins. The authors found antibodies against 10 out of 19 of the proteins two weeks after vaccination, showing an antibody-specific immune response. To further test the vaccine, the researchers placed black-legged ticks on the guinea pigs to assess if the bites would trigger an immune response. The vaccinated guinea pigs developed substantial redness around the tick bites in comparison to the unvaccinated guinea pigs which showed minimal redness. After 48 hours, some of the ticks began to detach from the vaccinated guinea pigs and 80% had completely detached after 96 hours. In a final experiment to test the vaccines’ ability to reduce the risk of Lyme disease, B. burgdorferi-positive ticks were placed on guinea pigs. In the unvaccinated guinea pig group, 6 out of 13 tested positive for B. burgdorferi but all of the vaccinated guinea pigs tested negative. This showed that not only could the vaccine mount an immune response against tick bites, it could also prevent the spread of Lyme disease in guinea pigs.

In my opinion, the study of dengue serotypes and tick mRNA vaccines present two crucially important areas in global host-pathogen interactions and infections. Understanding the patterns and differences between the dengue serotypes provides new insight into predicted outbreaks and potential treatments for those infected. The novel tick mRNA vaccine shows great potential at providing immunity to a variety of tick-borne pathogens that cause disease in humans. Future directions can focus on targeting the other 9 salivary proteins where immunity wasn’t detected in guinea pigs and then preparing the mRNA vaccine for humans.

References:

Sajid, A. et al. mRNA vaccination induces tick resistance and prevents transmission of the Lyme disease agent. Sci.Transl Med. https://doi.org/10.1126/scitranslmed.abj9827 (2021)

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Microbial Origins of Body Odor

lacydb1 — Wed, 23 Feb 2022 14:20:31 +0000

Microbial Origins of Body Odor lacydb1 Wed, 02/23/2022 - 08:20 RSS:

Elizabeth Semler

A rose in full bloom, a fresh pot of brewed coffee, and a raging bonfire are only three of the millions of scents that the human olfactory system can detect. While humans are able to distinguish between many different types of odors, not all are as pleasant as a rose in full bloom. Take for instance, bromhidrosis (i.e., body odor) – a common yet often unpleasant phenomenon in post-pubertal individuals. Human body odor is caused by many factors including sex, diet, health, and disease; however, the main contributor to body odor is due to the activity of bacteria on sweat glands^1-2.

Humans have three types of sweat glands: eccrine, apocrine and apoeccrine sweat glands, as well as sebaceous glands which influence the composition of sweat^1-3. Although eccrine sweat glands are the most ubiquitous and are responsible for the largest volume of sweat excretion, bromhidrosis is due to the interaction of apocrine sweat glands with various microorganisms^2-4. Unlike eccrine glands, apocrine sweat glands are restricted mainly to the axillary region, ear canals, the wings of nostrils and the perineal region. Apocrine glands produce an odorless fluid composed of proteins, lipids, fatty acids, branched-chain amino acids, vitamins, and steroids (i.e., sweat) that is discharged into the canals of hair follicles^2-4. It's not until the apocrine sweat is metabolized by axillary microorganisms such as Micrococcaceae, Propionibacteria, Staphylococcus and nondiptheiroid Corynebacterium species does it develop its characteristic odor^4-6.

A major odorant responsible for the onion-like malodor is generated mainly by Staphylococcus hominis, and is composed of volatile sulfur compounds such as 3-Methyl-3-sulfanylhexanol^3-6. These volatile sulfur compounds are secreted by apocrine glands as glycine-cysteine conjugates and are enzymatically cleaved by bacterial dipeptidases and C-S lyases which release odoriferous mercaptoalcohols^3-6. Other malodors include the volatile fatty acid 3-methyl-2-hexenoic acid (3M2H), which has a goat-like odor, and 3-methyl-3-hydroxy-hexanoic acid, which has a cumin like odor^3-6. Studies indicate that 3M2H is released from the skin surface after interacting with Corynebacterium striatum and Corynebacterium bovis^3-6. Another common malodor that is characterized by its vinegar-like smell is caused by Propionibacterium metabolizing glycerol and lactic acid, leading to the production of acetic and propionic acid^3-6.

The composition of the skin microbiota is diverse and can be functionally distinct between individuals. The skin microbiome and the volatile odorants produced are also dynamic and have been shown to shift in certain environments. Additionally, gastrointestinal ailments, various metabolic disorders, or even malaria can cause a change in the skin microbiome and odorants produced^3-6. It is therefore important to characterize the composition of the skin microbiome and the production of axillary odorants in health and disease, as it may lead to the development of novel diagnostic tools and therapeutic treatments.

References:

Kurosumi, K., Shibasaki, S., & Ito, T. (1984). Cytology of the Secretion in Mammalian Sweat Glands. International Review of Cytology, 253–329. doi:10.1016/s0074-7696(08)62445-6
Wilke K, Martin A, Terstegen L, Biel SS. A short history of sweat gland biology. Int J Cosmet Sci. 2007 Jun;29(3):169-79. doi: 10.1111/j.1467-2494.2007.00387.x.
Fredrich E, Barzantny H, Brune I, Tauch A. Daily battle against body odor: towards the activity of the axillary microbiota. Trends Microbiol. 2013 Jun;21(6):305-12. doi: 10.1016/j.tim.2013.03.002.
Mogilnicka I, Bogucki P, Ufnal M. Microbiota and Malodor-Etiology and Management. Int J Mol Sci. 2020;21(8):2886. doi:10.3390/ijms21082886
Byrd, A., Belkaid, Y. & Segre, J. The human skin microbiome. Nat Rev Microbiol 16, 143–155 (2018). https://doi.org/10.1038/nrmicro.2017.157
“Microbial Origins of Body Odor.” ASM.org,https://asm.org/Articles/2021/December/ Microbial-Origins-of-Body-Odor.

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Antibiotics and Antibiotic Resistance: from Past to Present

lacydb1 — Tue, 22 Feb 2022 14:11:47 +0000

Antibiotics and Antibiotic Resistance: from Past to Present

Class

lacydb1 Tue, 02/22/2022 - 08:11 RSS:

Emily Green

Imagine a world where infections that are currently viewed as minor were deadly, where your parent died from a burn that became infected with Staphylococcus aureus, or your friend lay suffering beside you on the battlefield with sepsis as you fought for the freedom of millions of wrongfully mistreated people. This world is not so far away or so distant in the past . While some parts of the world sadly still struggle with this, billions of people across the globe benefit annually from antibiotic treatment of formerly deadly, pathogenic infections. As Dr. Jim Cassat details in the lecture “In Case of Emergency: Bring Antibiotics!” the discovery of antibiotics is attributed to the research of many great scientists, a few accidents, and remains a current concern in the field of modern biomedical science.

The birth of clinical antibiotics is largely attributed to Sir Alexander Fleming who discovered penicillin after neglecting plates in the lab during the summer of 1928. Upon returning to the lab in the fall, he discovered a mold on the agar plates he had used months prior and began investigating the organism. Following his studies into the mold Penicillium notatum, Fleming published his findings a year later. While Fleming’s discovery would go on to spur a radical change in clinical microbiology, he was not the first to describe antibiotics, nor the reason for the change in production scaling that would lead to penicillin’s clinical relevance, as stressed by Dr. Cassat.

By 1945, penicillin ushered in the “Golden Age of Antibiotics” thanks to three English scientists- Howard Florey, Norman Heatley, and Ernst Chain, who worked to purify and amplify production of penicillin, thus allowing it to be produced in clinically relevant quantities for use during World War II (1). Fleming, Florey, and Chain were awarded a Nobel Prize in 1945, seventeen years after penicillin was first discovered. In his Nobel lecture, Fleming recognized and warned of the danger of widespread antibiotic use:

“It is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body. The time may come when penicillin can be bought by anyone in the shops. Then there is the danger that the ignorant man may easily underdose himself and by exposing his microbes to non-lethal quantities of the drug make them resistant.” (2).

Fleming’s warning may have been issued the better part of a century ago, but the very words he spoke resonate the urgency of current clinical antibiotic resistance. In 2019, some U.S. states exceeded 920 antibiotic courses prescribed per 1,000 patients in clinics alone (3). Other countries such as India have unregulated antibiotics available without prescription, and agriculture across the globe has leveraged antibiotics to produce more food per acre/head. Together, the world faces an ever-increasing health threat. The CDC reports that as of 2021, 2.8 million antibiotic resistant infections occur annually in the U.S. (4). Antibiotic use must be decreased and appropriated in an effort to alleviate selective pressures on bacterial populations and decrease the evolution of antibiotic resistance. This is an ever-growing issue considering that pharmaceutical companies are moving away from antibiotic production due to hospitals reserving new compounds for the most dire of cases, according to Dr. Cassat. In combination with a decrease in antibiotic discovery and production, the world faces a clinical crisis. If we continue to ignore Fleming’s warning, will we force ourselves to return to a near pre-antibiotic world?

References:

Quinn R. (2013). Rethinking antibiotic research and development: World War II and the penicillin collaborative. American journal of public health, 103(3), 426–434. https://doi.org/10.2105/AJPH.2012.300693
Sir Alexander Fleming. (1945). Nobel Lecture. NobelPrize.org. Nobel Prize Outreach AB 2022. https://www.nobelprize.org/prizes/medicine/1945/fleming/lecture
Centers for Disease Control and Prevention. (2021, November 1). Current report. Centers for Disease Control and Prevention. Retrieved February2022, from https://www.cdc.gov/antibiotic-use/stewardship-report/current.html
Centers for Disease Control and Prevention. (2021, November 23). Tracking antibiotic resistance. Centers for Disease Control and Prevention. Retrieved February 2022, from https://www.cdc.gov/drugresistance/tracking.html

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Viruses can do that too?

lacydb1 — Wed, 10 Feb 2021 01:58:05 +0000

Viruses can do that too? lacydb1 Tue, 02/09/2021 - 19:58 RSS:

Microbial_wanderlust

Bacteriophages, or phages, are a type of virus that specifically target bacteria for resources and reproduction¹. The diversity of phages in size, functional capability, and genetic information is exponentially increasing as more are discovered and characterized. In general, phage infect a specific species of bacteria. Almost all phages have similar structures, consisting of a capsid “head” that stores genetic information and a “tail” that is used to interact with a host. Like other viruses, phages do not have a nucleus. However, it was discovered by Vorrapon Chaikeeratisak et al. in 2017 that a set of phages that specifically infect Pseudomonas species were observed with a proteinaceous, nucleus-like compartment, or “shell”, that surrounded the phage DNA2. An example of this can be seen in Figure 4A from the paper, where they used cryo-electron tomography to show an infected cell that contained phage with the shell, represented by the phage that are darker in color.

This preliminary finding influenced the work of Senén Mendoza from the Bondy-Denomy group, who normally study CRISPR-Cas biology and function. In 2020, Mendoza and others published a paper entitled “A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases”, where they find that the previously studied “shell” can actually protect phage DNA from degradation by host CRISPR machinery³. In this study, they found that DNA the large phage ΦKZ, which exclusively infects Pseudomonas aeruginosa and was part of the earlier group of phages studied by Chaikeeratisak, was unaffected when the phage was challenged with an array of CRISPR enzymes. Some phages that infect P. aeruginosa have been previously shown to block CRISPR enzymes through the production of inhibitory proteins. However, the authors performed a genome-wide search and discovered that ΦKZ did not encode for any of these proteins. Through the use of fluorescence microscopy, they were able to show that different CRISPR-Cas enzymes are unable to breach the “shell”, as shown here in Figure 2b from the paper. Here, the first column shows CRISPR enzymes labeled with mCherry and the second column shows phage DNA stained with DAPI. They also explain that, when removed from the “shell”, ΦKZ phage DNA is able to be cleaved by CRISPR enzymes, indicating that the lack of degradation is not due to an intrinsic feature of the DNA. Finally, the authors created a fusion protein of different CRISPR enzymes to a host protein involved in DNA replication that had been known to bypass the “shell”, though the specific mechanism by which this is achieved is unknown. This resulted in cleavage of ΦKZ DNA, again indicating that the nucleus-like compartment is what confers resistance to CRISPR enzymes.

The authors conclude that this discovery speaks to the larger trend of growing phage diversity and highlights a unique and intriguing point of evolution in the viral realm. They propose that this shell could be observed in other, large phages that are not specific to Pseudomonas sp. One area in which the authors plan to continue researching is understanding how the “shell” selectively permits which enzymes are able to reach the phage DNA. This paper represents one of a growing number of reports that highlight unique features of viruses that defy expectations.

References

1. Kasman LM, Porter LD. Bacteriophages. [Updated 2020 Oct 1]. In: StatPearls [Internet]. Treasure Island (FL): StatPearls Publishing; 2020 Jan-. Available from: https://www.ncbi.nlm.nih.gov/books/NBK493185/

2. Mendoza, Senén D., et al. "A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases." Nature 577.7789 (2020): 244-248.

3. Chaikeeratisak, Vorrapon, et al. "Assembly of a nucleus-like structure during viral replication in bacteria." Science 355.6321 (2017): 194-197.

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Skin microbiota: Roles in barrier maintenance & repair

lacydb1 — Tue, 09 Feb 2021 02:45:59 +0000

Skin microbiota: Roles in barrier maintenance & repair lacydb1 Mon, 02/08/2021 - 20:45 RSS:

Teresa Torres, @tsosciency

In recent years, the human microbiome began to be considered one of the major organs of the human body; it is defined as the collection of all the microorganisms living in symbiosis with the body (Human Microbiome Project, NIH). The microbiome found on and within the human body comprises about one to three percent of the body’s mass and is composed of various communities including, eukaryotes, archaea, bacteria and viruses which outnumber cells in the body due to their miniscule size. As the microbe-host field continues to grow, the literature strongly implicates a link between microbial composition of the microbiome an how it may relate to numerous disease states, as well as giving a growing implication that manipulation of these microbial communities may be a potential avenue for treatment of disease.

Recently, Dr. Grice, an associate professor at the University of Pennsylvania, gave a talk for the VI4 seminar series introducing the skin microbiome as a protective barrier and a source of repair when working together with other host mechanisms of protection like innate and adaptive immune responses. The skin is able to support the growth of microorganisms due to the nutrients that are provided by the sebum released from the sebaceous gland which serves to emolliate our skin. Her research program focuses on understanding the role of the skin microbiome in skin diseases by bringing together culture-independent and culture-based approaches. The Grice lab is interested in understanding the homeostatic roles of the commensal skin microbiota and how alteration influence integrity and function of skin. To answer these questions, she has various ongoing projects in her lab; one of these projects focuses on understanding what genes during skin homeostasis are regulated specifically by the skin microbiome. A graduate student apart of the Grice lab was able to investigate this particular interest further through the use of a gnotobiotic mouse model. Comparing gene regulation of over 700 genes between specific pathogen free and germ-free mice, they were able to observe regulation of certain genes belonging to the epidermis complex. To follow up, a postdoctoral fellow, did a RNAseq study that looked into the gene ontology of the epidermis complex to better understand what pathway were affected by the skin microbiome. Their data revealed that skin and epidermal development as well as keratinocyte differentiation were heavily influenced if not regulated by the skin microbiome. It is important to note that their data was indicative of Currently they have several follow-up projects focusing on understanding what the morphological and functional implications of dysregulated gene expression when the skin microbiome is disrupted.

In 2020 the Grice Lab published an article in the journal Cell Host & Microbe, where they discussed protective factors of the skin microbiome and its role in pathogen colonization resistance against bacterial microorganisms like Staphylococcus aureus. They focus on this specific pathogen because S. aureus is the leading cause for skin and soft tissue infections in the United States. The authors focused on understanding the direct and indirect protective responses provided by the skin microbiome during pathogen invasion. Their data demonstrates the direct protective factors of certain skin microorganisms like Staphylococcus epidermis which are able to produce antimicrobials and tolerate an immune response provide protection against S. aureus invasion of the skin during infection (Flowers and Grice, 2020). In a more indirect way, commensal microorganisms of the skin are able to stimulate host cells into prompting a host immune response (Flowers and Grice, 2020).

I really enjoyed Dr. Grice’s seminar because it provided insight about a part of the body that has huge microbiota implications and often is not thought about. I look forward to what other fascinating results come from her lab and how it may pertain to the role of the skin microbiota in the development of skin cells. As the microbiome field continues to evolve, it is interesting to see how microorganisms may affect key roles in development and protection.

References

Human Microbiome Project. https://commonfund.nih.gov/hmp. August 2020.
Flowers L, Grice EA. “Skin microbiota: Roles in barrier maintenance & repair.” VI4 Seminar. January 12, 2021.
Flowers L, Grice EA. The Skin Microbiota: Balancing Risk and Reward. Cell Host Microbe. 2020 Aug 12;28(2):190-200. doi: 10.1016/j.chom.2020.06.017. PMID: 32791112; PMCID: PMC7444652.

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Alcanivorax, an efficient cleaner of our oceans

lacydb1 — Tue, 09 Feb 2021 02:21:01 +0000

Alcanivorax, an efficient cleaner of our oceans lacydb1 Mon, 02/08/2021 - 20:21 RSS:

Steven Wall

Our oceans are chock-full of microbes, from the clear blue waters to the darkest depths. In fact, the reason ocean water is so clear in some areas is due to the nearly perfect utilization of nutrients in the water. Even though many people might find the thought of bacteria disgusting, they are invaluable members of marine ecosystems. Along with other microbial life, they are responsible for the majority of the nutrient cycling that keeps everything in homeostasis.¹ It is usually when humans mess things up by polluting the environment that problems occur.

It is common knowledge that hydrocarbons like plastics and crude oil are major sources of pollution in our oceans. Plastics are such a large pollutant that there is a mass in the Pacific ocean known as the “Pacific Garbage Patch” that has been exponentially growing in size for decades, with some estimates placing it as being larger than many countries.² In a recent article from the blog Small Things Considered, authors Joseph A. Christie-Oleza and Vinko Zadjelovic discuss a fascinating group of bacteria that they call a “brigade of microbial cleaners”, known scientifically as obligate hydrocarbonoclastic bacteria (OHCB).³ This simply means that they need to consume hydrocarbons in order to survive. Alcanivorax is one such bacterial genus that belongs to this brigade, and it is the most well studied of the bunch. Because of the niche these bacteria occupy, they exist in very low populations in ecosystems with no pollution. It was unknown for a time how they survive for long periods of time without any sort of pollution to sustain them. It turns out that cyanobacteria, which are the most plentiful photosynthesizers on the planet, produce alkanes that are able to sustain these OHCBs at a very low level.

The reason that OHCBs like Alcanivorax can degrade alkanes is through a specific type of enzyme known as a monooxygenase. With the help of these enzymes, OHCBs are able to oxidize long chain alkanes, such as those in crude oil, that would otherwise be unusable. Once oxidized they can flow into the beta oxidation pathway to serve as a carbon source. One of the potential limitations of OHCBs that the authors mention is that it is currently unclear if they can degrade extremely long chain polymers such as polyethylene that make up a large percentage of plastic waste in the oceans, however the authors seem hopeful. In a recent paper by the same authors, they showed experimentally that Alcanivorax was capable of efficiently degrading synthetic aliphatic polyesters. Like polyethylene, polyesters are extremely long chain plastic polymers, but Alcanivorax is able to metabolize polyesters with a special type of secreted esterase that breaks up the long chain into smaller subunits that the bacteria can utilize.⁴ Importantly, these aliphatic polyesters are thought of widely as being more biodegradable and eco-friendly and, as the authors say, now we know that the ocean has a way of dealing with them.

The ramifications of this research are far reaching. Alcanivorax shows us that the microbial world has an untapped arsenal of powerful tools for solving problems that we are still struggling with. We just need to put the money and effort in to finding these microbes. It’s pretty amazing that the ocean microbiome has coevolved in this way to keep these OHCBs as a reserve emergency custodial force, ready to ramp up and do their part.

References

Sigman, D. M. & Hain, M. P. (2012) The Biological Productivity of the Ocean. Nature Education Knowledge 3(10):21
Lebreton, L., Slat, B., Ferrari, F. et al. Evidence that the Great Pacific Garbage Patch is rapidly accumulating plastic. Sci Rep 8, 4666 (2018). https://doi.org/10.1038/s41598-018-22939-w
Christie-Oleza J. A. & Zadjelovic V. “Alcanivorax, an efficient cleaner of our oceans.” Small Things Considered, 2020, https://schaechter.asmblog.org/schaechter/2020/12/alcanivorax-an-efficient-cleaner-of-our-oceans.html
Zadjelovic, V., Chhun, A., Quareshy, M., Silvano, E., Hernandez‐Fernaud, J.R., Aguilo‐Ferretjans, M.M., Bosch, R., Dorador, C., Gibson, M.I. and Christie‐Oleza, J.A. (2020), Beyond oil degradation: enzymatic potential of Alcanivorax to degrade natural and synthetic polyesters. Environ Microbiol, 22: 1356-1369. https://doi.org/10.1111/1462-2920.14947

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The Superpowers of P. luminescens

lacydb1 — Mon, 08 Feb 2021 02:46:18 +0000

The Superpowers of P. luminescens lacydb1 Sun, 02/07/2021 - 20:46 RSS:

Kateryna N.

The richness of the bacterial world is truly astonishing. While it is impossible to know an exact number of bacterial species on our planet, some reports help us appreciate the scope of the bacterial diversity. According to Nature Reviews, “there are 100 million times as many bacteria in the oceans (13×10²⁸) as there are stars in the known universe”.¹ Other studies suggest that the Earth is home to 1 trillion (10¹²) microbial species.² Considering that scientists have been able to investigate and culture only ~30,000 bacterial species³, one can conclude that the fraction of the bacterial population that has been sampled so far is relatively low. It is thus remarkable how much interesting and distinct information we have learned from this relatively small representative sample of bacteria around us. Photorhabdus luminescens is a great example of a bacterium that has unique physiology, clinical and agricultural relevance, and potentially even a role in history. During our introductory lecture by Dr. Hadjifrangiskou, we briefly heard about P. luminescens which caught my attention by its natural ability to luminesce. It turns out, there is much more to it than that.

The life cycle of P. luminescens is quite a story. The bacterium lives in symbiosis with the nematode Heterorhabditis bacteriophora.⁴ When the nematodes infect insects and enter their bloodstream, they release P. luminescens.⁴ The bacteria subsequently secrete toxins and enzymes that decompose the insect carcass.⁴ As a result, the symbiotic duo has food for survival and reproduction.⁴ Eventually, the nematodes and bacteria reassociate, emerge from the carcass, and start looking for a new insect host.⁵ Interestingly, according to some stories, this symbiotic relationship even had a role in the Battle of Shiloh during the American Civil War.⁶ It was noticed that some soldiers’ wounds began to glow in the dark, and those with glowing wounds recovered much faster.⁷ Although this might have been a folklore legend, an explanation for this observation, sometimes referred to as “angel’s glow”, was later provided.⁷ It was proposed that, in some cases, insects attracted to soldiers’ wounds were infected with the nematodes carrying P. luminescens.⁷ As a result, the luminescent bacteria got released into the soldiers' wounds causing the glowing effect.⁷ Nowadays, it is also known that P. luminescens produce many antimicrobial substances against bacterial competitors.⁵ Thus, P. luminescens could inhibit the growth of other bacteria in open wounds leading to soldiers’ recovery. The breadth of P. luminescens’ capabilities is fascinating to me!

Besides its clinical relevance, P. luminescens is relevant to agriculture due to its role in insect control.⁴ For example, insect-pathogenic nematodes carrying Photorhabdus species have been used as biopesticides in the United States and Australia.⁴ Overall, this story made me conclude: the bacterial diversity is striking, but so is the diversity of functions within just one bacterial species, such as P. luminescens.

References:

(1) (2011) Microbiology by numbers. Nat. Rev. Microbiol. 9, 628.

(2) Locey, K. J., and Lennon, J. T. (2016) Scaling laws predict global microbial diversity. Proc. Natl. Acad. Sci. 113, 5970 LP – 5975.

(3) Dykhuizen, D. (2005) Species Numbers in Bacteria. Proc. Calif. Acad. Sci. 56, 62–71.

(4) Gerrard, J. G., McNevin, S., Alfredson, D., Forgan-Smith, R., and Fraser, N. (2003) Photorhabdus species: bioluminescent bacteria as emerging human pathogens? Emerg. Infect. Dis. 9, 251–254.

(5) Heermann, R., and Fuchs, T. M. (2008) Comparative analysis of the Photorhabdus luminescens and the Yersinia enterocolitica genomes: uncovering candidate genes involved in insect pathogenicity. BMC Genomics 9, 40.

(6) Youle, M. (2009) The Two Faces of Photorhabdus. Small Things Consid.

(7) Durham, S. (2001) Students May Have Answer for Faster-Healing Civil War Wounds that Glowed. ARS News Inf.

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A Microbe You May Not Know

lacydb1 — Sun, 07 Feb 2021 21:56:56 +0000

A Microbe You May Not Know lacydb1 Sun, 02/07/2021 - 15:56 RSS:

Clostridium bonelium

On this episode of the podcast “This Week in Microbiology” Vincent Racaniello, Elio Schaechter, Michele Swanson, and Michael Schmidt discussed the research paper from the National Institute of Allergy and Infectious Disease (NIAID) by Myles et al. titled “Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair” which discussed the skin microbiome and atopic dermatitis. Michael Schmidt remarked how impactful a probiotic treatment for atopic dermatitis can be for an individual’s physical health and their psyche. The clinical data were followed by a mechanistic exploration of how R. mucosa affects the epithelium. Contrary to the organization of most scientific papers, this paper begins with a discussion of the clinical data followed by the basic research that lead to the clinical trial.

Myles et al. explored the utilization of R. mucosa obtained from healthy individuals as a topical probiotic for individuals suffering from atopic dermatitis. Individuals with this disease contain R. mucosa in their skin microbiota; however, the R. mucosa varies from that of healthy individuals. This variation in the skin microbiota causes skin inflammation resulting in irritation and in some instances, lesions. Participants in the clinical trial were scored before and after application of cultured R. mucosa using existing clinical scales (SCORAD and EASI). Additionally, the authors used dose escalation in the trial which increased the concentration of R. mucosa over time. There was significant improvement in all patients compared to the placebo and an FDA approved drug Tacrolimus (Myles et al., 2020). This represents a great alternative to Tacrolimus and other immunosuppressive medication. Michele Swanson mentioned that the primary author involved in the clinical trial noticed a change in patient behavior. Specifically, R. mucosa probiotic treatment improved children’s self-confidence, which was observed by changes in behavior such as wearing short-sleeve shirts.

Following the results of the clinical investigation, the hosts discussed the mechanistic success of the probiotic described by the authors of the study. The microbiome of the skin was tracked over time during the clinical trial. Application of R. mucosa resulted in an increase in Alphaproteobacteria and a subsequent decrease in Staphylococcaceae abundance. The altered microbial populations resemble that of the skin found in healthy individuals. Cytokine levels from the skin showed anti-inflammatory properties such as IL-13 and TNFa (Myles et al., 2020). Following molecular characterization of patients’ healing tissue, the authors assessed tissue repair in cell culture. A scratch was mimicked in co-culture with keratinocytes and R. mucosa from either healthy or atopic dermatitis individuals. Keratinocytes co-cultured with R. mucosa from healthy individuals proliferated and “healed” the scratch faster, whereas co-cultures with R. mucosa from atopic dermatitis individuals did not affect keratinocyte growth. Exploring transcriptomics, quantitative enzymatic comparison, and metabolomics between R. mucosa from individuals with and without atopic dermatitis, the authors found differences in each experimental approach regarding glycerophospholipid production. In cell culture, keratinocytes were treated with lipids isolated from R. mucosa of healthy individuals. Similar increases in keratinocyte growth were observed when cells were treated with lipids or cultured with R. mucosa from healthy individuals. However, when keratinocytes were treated with a lipase after lipid addition, the increase in growth was ablated (Myles et al., 2020). The podcast hosts presented a very unique and impactful study detailing basic research and clinical trial data in a fun and interactive format for all audiences.

References

Myles, I. A., Castillo, C. R., Barbian, K. D., Kanakabandi, K., Virtaneva, K., Fitzmeyer, E., ... & Datta, S. K. (2020). Therapeutic responses to Roseomonas mucosa in atopic dermatitis may involve lipid-mediated TNF-related epithelial repair. Science translational medicine, 12(560).

Schmidt, M., Swanson, M., Schaechter, E., Racaniello, V. (2020). Two microbes you might not know (No. 226). https://www.microbe.tv/twim/twim-226/

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The Story of Antibiotics and Bacterial Resistance

lacydb1 — Sat, 06 Feb 2021 18:38:42 +0000

The Story of Antibiotics and Bacterial Resistance lacydb1 Sat, 02/06/2021 - 12:38 RSS:

Abbie Weit

In the lecture taught by Dr. James Cassat, our class learned about the history of antibiotic discovery. The timeline started with penicillin which was discovered by Alexander Fleming. After a vacation to Scotland in 1928, Fleming returned to his lab to find a plate of staphylococcus that had been left out on the bench. The plate was contaminated with a mold that he hypothesized was secreting something that killed the staph. Since it was difficult to extract the secretion from the plate, Professors Florey, Chain, and Heatley figured out the technique and resources to do so successfully. This led to major use of penicillin in treating infections in World War II soldiers.^1,3 Penicillin also started the golden age of antibiotic discovery. Discoveries that followed included prontosil by Gerhard Domagk who successfully treated his daughter with sepsis. The Soviets isolated streptomycin from soil which was the first antibiotic that was active against tuberculosis. Another antibiotic extracted from a soil sample was tetracycline which was used to treat fevers, skin infections, and respiratory infections.² This explosion of antibiotics continued until around the 1990s when there was what Dr. Cassat referred to as the “discovery void of antibiotics”. Dr. Cassat believes we may be entering a second golden age of antibiotics, yet they are not as widely used and profitable as before due to the phenomenon of antibiotic resistance.

Although antibiotics are a great resource for treatment of various infections, microorganisms quickly develop a defense or resistance to these drugs making them less effective. The main cause of antibiotic resistance is overuse of antibiotics.³ This can occur spontaneously through mutations.⁴ Also, genes are inherited or passed between non-relative bacteria which is a process called horizontal gene transfer.⁴ Because resistance spreads so easily, it is crucial for physicians to only prescribe antibiotics when necessary. However, that is often not the case. In 2010, many U.S. states prescribed antibiotics more times than the number of people in the state.⁵ Studies also show that antibiotic treatments are wrong or unnecessary in 30-50% of cases.³ Antibiotic resistance is projected to cause ten million deaths by 2050 as noted by Dr. Cassat.⁶ The best ways that physicians can decrease resistance is by not treating asymptomatic infections⁴ and exhausting all other treatment options before using antibiotics.

A major caveat of physicians using less antibiotics is the resulting decrease in revenue for suppliers. Dr. Cassat stated that many of these therapeutics sit on hospital shelves for just periodic, necessary cases which results in little demand for the product. Therefore, it is quite hard for pharmaceutical companies to make profit on antibiotic treatments.⁶ This prevents companies from pursuing opportunities for developing new antibiotics leading to a lack of progression in this field. Dr. Cassat believes that academic research of antibiotics is at the level of a second golden age. However, it is difficult to get these exciting developments to reach the clinic due to companies not wanting the financial risk. I firmly agree with Dr. Cassat’s view that federal and state funding should be used to support companies aiming to bring these drugs to market so that physicians may continue using antibiotics sparingly. Therefore, new antibiotics will continue to be produced yet we can slow down future antibiotic resistant-related deaths simultaneously.

Sengupta, S., Chattopadhyay, M. K., & Grossart, H. P. (2013). The multifaceted roles of antibiotics and antibiotic resistance in nature. Frontiers in Microbiology. Frontiers Research Foundation. https://doi.org/10.3389/fmicb.2013.00047
Tetracycline: MedlinePlus Drug Information. (n.d.). Retrieved January 13, 2021, from https://medlineplus.gov/druginfo/meds/a682098.html
Ventola, C. L. (2015). The antibiotic resistance crisis: causes and threats. P & T Journal, 40(4), 277–283. https://doi.org/Article
Read, A. F., & Woods, R. J. (2014). Antibiotic resistance management. Evolution, Medicine and Public Health, 2014(1), 147. https://doi.org/10.1093/emph/eou024
Gross, M. (2013). Antibiotics in crisis. Current Biology, 23(24). https://doi.org/10.1016/j.cub.2013.11.057
Plackett, B. (2020, October 1). Why big pharma has abandoned antibiotics. Nature. NLM (Medline). https://doi.org/10.1038/d41586-020-02884-3

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A Whiff of Taxonomy – The Apicomplexa by Moselio (Elio) Schaechter

lacydb1 — Sat, 06 Feb 2021 18:26:06 +0000

A Whiff of Taxonomy – The Apicomplexa by Moselio (Elio) Schaechter lacydb1 Sat, 02/06/2021 - 12:26 RSS:

CVRVC

Apicomplexa are a phylum of parasitic alveolates that get their name from the presence of the apical complex. The apical complex consists of many microtubules and secretory organelles, such as the micronemes and the rhoptries. Additionally, an organelle, the apicoplast, contains its own DNA and is considered a derivative of chloroplasts in plants. Micronemes secrete proteins known as microneme proteins (MICs) which are vital in the initial stages of host cell invasion by parasites (Foroutan 2018). Rhoptries undergo exocytosis upon host cell invasion and their proteins are involved in creating the moving junction that propels the parasite in the cell and in building the parasitophorous vacuole in which the parasite develops (Dubremetz, 2007).

Apicomplexa’s main goals are to reproduce rapidly and produce a large amount of progeny to exist for a long time, and to successfully enter a host organism. They achieve this by asexual reproduction based on where new parasites are formed. When daughter parasites are formed inside the parent the process is called endodyogeny/endopolygeny, while budding from the mother plasmalemma (cell membrane) is called schizogony. When Apicomplexa species enter a host organism, they can cause various life-threatening diseases to human and animals.

Apicomplexan parasites such as Toxoplasma gondii, Plasmodium spp, and Cryptosporidium are leading causes of human and livestock diseases—like toxoplasmosis, malaria, and severe diarrhea, respectively (Checkley, 2015). Toxoplasma gondii is an intracellular protozoan parasite of global importance that can remarkably infect, survive, and replicate in nearly all mammalian cells (Lima, 2019). Many infections caused by Toxoplasma gondii are asymptomatic, but can be very life-threatening infections. According to the CDC, toxoplasmosis is a leading cause of death caused by foodborne illness in the United States where more than 40 million men, women, and children in the U.S. carry the Toxoplasma parasite. Temperature is a key factor influencing the invasion and proliferation of Toxoplasma gondii in fish cells (Yang, 2020). Plasmodium spp have infected more than 300 to 500 million individuals worldwide, and 1.5 to 2.7 million people a year, most of whom are children, die from the infection (Garcia, 2010). Malaria is transmitted by mosquitoes carrying a specific parasite. People with malaria often experience fever, chills, and flu-like illness. Malaria was found to be caused by the 4 most common Plasmodium spp that infect humans, P. vivax, P. ovale, P. malariae, and P. falciparum (Garcia, 2010). The CDC described Cryptosporidium as a parasite that infects both animals and humans. The parasite is protected by an outer shell that allows it to survive outside the body for long periods of time and makes it very tolerant to chlorine disinfection, hence, making water an easy spreader. Apicomplexan diseases are life-threatening, and infections should be ultimately avoided. In case of infection, treatments such as antibiotics, should be utilized to prevent death.

References

Checkley W, White AC, Jaganath D, Arrowood MJ, Chalmers RM, Chen XM, Fayer R, Griffiths JK, Guerrant RL, Hedstrom L, et al. A review of the global burden, novel diagnostics, therapeutics, and vaccine targets for cryptosporidium. Lancet Infect Dis. 2015; 15:85–94.

Dubremetz, JF. 2007. Rhoptries are major players in Toxoplasma gondiiinvasion and host cell interaction. Cellular Microbiology (2007) 9(4), 841–848

Foroutan M, Zaki L, Ghaffarifar F. 2018. Recent progress in microneme-based vaccines development against Toxoplasma gondii. Clin Exp Vaccine Res. 7(2):93-103. doi: 10.7774/cevr.2018.7.2.93.

Garcia, LS. 2010. Malaria. Clinical Lab Med. 30(1):93-129.doi: 10.1016/j.cll.2009.10.001.

Lima, TS and Lodoen, MB. 2019. Mechanisms of Human Innate Immune Evasion by Toxoplasma gondii. Front. Cell. Infect. Microbiol. 9:103. doi: 10.3389/fcimb.2019.00103

Yang Y, Yu SM, Chen K, Hide G, Lun ZR, Lai DH. 2020. Temperature is a key factor influencing the invasion and proliferation of Toxoplasma gondii in fish cells. Exp Parasitol.217:107966. doi: 10.1016/j.exppara.2020.107966.

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“Staying Healthy: Hide Your Metal”

lacydb1 — Wed, 03 Feb 2021 14:19:35 +0000

“Staying Healthy: Hide Your Metal” lacydb1 Wed, 02/03/2021 - 08:19 RSS:

Eki

Earlier this month, in the class lecture, "Staying Healthy: Hide Your Metal", Dr. Jennifer Gaddy introduced the importance of metal ion homeostasis, an important balance in which cells must keep an adequate level of metals that serve as cofactors for various enzymes and other proteins, but also, avoid metal ion intoxication (Chandrangsu et al., 2017). Metal ions are essential for several cellular processes such as cellular growth, cellular respiration, and stress responses. The vertebrate host serves as a rich source of nutrient metals for all microorganisms, which have a strict growth requirement for transition metals, which is around 10 ^-6 – 10 ^-8M. In addition to cellular growth, bacteria require cofactors for stress responses. When bacteria encounter environmental stressors, cytoplasmic enzymes are essential for repressing the stressors. The host vertebrate's common stressors are reactive oxygen species (ROS), which are highly reactive molecules that are generated during mitochondrial oxidative metabolism. However, several enzymes used to break down harmful ROS are called superoxide dismutase (SOD), and they use an array of metal cofactors such as manganese, iron, zinc, and copper. In the case of the finite number of metals, SOD is not functional and cannot detoxify ROS. Accumulation of ROS can be detrimental for the host and may damage nucleic acids, proteins, and other cellular components. Another topic covered during the lecture was cellular respiration, a set of metabolic reactions and processes in which cells convert chemical energy from oxygen or nutrients into adenosine triphosphate (ATP). During respiration, the electrons are transferred by reduction/oxidation or by cytochromes oxidase complex via catalysis, in which the free energy generated by electron transfer is utilized by ATP synthase. The final step in the process is catalyzed by complex IV (cytochrome oxidase), where electrons are transferred from cytochrome c to the molecular oxygen, which serves as the terminal electron acceptor in aerobic respiration. Cytochromes have various cofactors necessary for cellular respiration, such as ferric sulfur clusters, iron-sulfur clusters, copper centers, and the main requirement is heme (Landolfo, 2008).

Vertebrate immune systems developed revolutionary defense mechanisms in order to protect invading pathogens. Nutritional immunity is when the host exploits microbial requirements for transition metals by sequestering them to limit pathogenicity during the infection. Concentrations of metals, such as iron and zinc, decline fast during the infection, and the reason for it is to starve invading pathogens of these essential elements (Begg, 2019). Nutritional immunity is regulated by several proteins such as S-100A, transferrin, lactoferrin, heme, and hemoglobin. The large S-100A family of calcium-binding proteins are found in vertebrates and are important for defense against infection since many S-100A proteins have antimicrobial properties. One of the best-studied is calprotectin (S100A8/A9), which makes up approximately 40% of the neutrophil cytoplasm's protein composition and can bind zinc, manganese, iron, and copper. Another vital protein, S-100A12, also known as calgranulin C, binds both zinc and copper and is involved in generating superoxide species. Studies have shown that genetic mutation in the metal-binding sites of S-100A proteins disrupts proteins' antimicrobial activity. Lactoferrin and transferrin, dual-lobed multifunctional glycoproteins found in a vertebrate, bind and mediate the transport of iron through the blood plasma. Increasing concentrations of lactoferrin and transferrin inhibit the growth of various pathogens over time. Most of the body's iron is found in the Red Blood Cells (RBCs), specifically in protein hemoglobin, which is essential for transferring oxygen in the blood. Hemoglobin comprises four polypeptide chains, two alpha and two beta chains, with each chain attached to a heme group composed of a porphyrin ring attached to an iron atom.

To bypass metal starvation, microorganisms deploy metal piracy systems, such as siderophores, zincophores, and cuprophores, to exploit the transition metals. Siderophores, zincophores, and cuprophores are low molecular weight compounds that can bind transition metals with high affinity. Deployment of toxins, such as hemolytic toxins, is another mechanism to bypass metal starvation. Hemolytic toxins destroy RBCs and release free hemoglobin, which is then degraded by hemoglobin protease to release heme, following secretion of hemophores, which capture heme and shuttle it across the membrane. Additionally, in response to zinc starvation, bacteria can alter their outer membrane, which causes biofilm formation. Lastly, Dr. Gaddy concluded the lecture by talking about metal toxicity. Metal toxicity can cause protein denaturation, disrupt the cell membrane, inhibit transcription and cell division, and inhibit enzyme activity. One of the most common deleterious effects of metal toxicity is mismetallation, which results in enzyme activity inhibition because the wrong ion has replaced the correct cofactor. Bacteria respond to metal toxicity by deploying efflux pumps to exclude metal ions out of the cell. Recent studies have shown that bacteria can highjack host metal-binding proteins to help mitigate metal toxicity.

References

Chandrangsu, P., Rensing, C. & Helmann, J. Metal homeostasis and resistance in bacteria. Nat Rev Microbiol 15, 338–350 (2017). https://doi.org/10.1038/nrmicro.2017.15
Begg SL. The role of metal ions in the virulence and viability of bacterial pathogens. Biochem Soc Trans. 2019 Feb 28;47(1):77-87. doi: 10.1042/BST20180275. Epub 2019 Jan 9. PMID: 30626704.
Sara Landolfo, Huguette Politi, Daniele Angelozzi, Ilaria Mannazzu, ROS accumulation and oxidative damage to cell structures in Saccharomyces cerevisiae wine strains during fermentation of high-sugar-containing medium, Biochimica et Biophysica Acta (BBA) - General Subjects, Volume 1780, Issue 6, 2008, Pages 892-898, ISSN 0304-4165, https://doi.org/10.1016/j.bbagen.2008.03.008.

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