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A list of the microbiome superstar species

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Darko Savic
Darko Savic Sep 21, 2020
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Necessity

Is the problem still unsolved?

Conciseness

Is it concisely described?

Let's compose a list of the most valuable microbial species that live within the human body

  • name the species
  • which part of the body does it live on
  • How does it help us? Explain what benefit it provides to the host body (preferably with a reference included).
8
Creative contributions

lactobacilli

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Michael Edwards
Michael Edwards Sep 21, 2020
survives in the stomach and intestines, produces lactic acid which is damaging to potentially harmful microbes.
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Jurana year ago
Hopefully, these amazing pals do much more. Here are some papers showing that certain strains help to slow down skin aging. http://www.jmb.or.kr/submission/Journal/025/JMB025-12-24_FDOC_1.pdf https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084287/
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Enterobacteraceae

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Michael Edwards
Michael Edwards Sep 21, 2020
GI tract responsible for helping produce vitamin K.
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Escherichia coli

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Povilas S
Povilas S Sep 21, 2020
It’s often associated with diseases, but most strains of E. coli are harmless and live in human intestine since we are babies. Those are considered commensals (neutral to humans), but many researchers point out benefits of E. coli: they can prevent gut inflammation [1] and colonization of the gut with pathogenic bacteria [2]. Certain strains of this bacteria are used as probiotics and have been proven to decrease the risk of allergies and infections [3], [4]. Certain strains are also capable of producing vitamin K2 [5]. And many more interrelations and positive influences for human body may just be overlooked and not understood yet, this bacteria is very intrinsic to humans, so it’s not trivial to presume that removal of it from our guts would cause serious health problems. [1] https://academic.oup.com/ibdjournal/article/11/5/455/4683971 [2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1728375/ [3] https://www.karger.com/Article/Abstract/71488 [4] https://akjournals.com/view/journals/1886/6/3/article-p147.xml [5] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC281544/pdf/microrev00014-0005.pdf
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Yeasts

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Michael Edwards
Michael Edwards Sep 21, 2020
Survives on the skin and in the GI tract produces alcohol which kills other microbes reducing their chance of infecting a person, also converts sugars into proteins.
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Darko Savic
Darko Savica year ago
Which specific species are beneficial though? Some also cause problems like athlete's foot, etc
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Streptococcus mutans engineered against dental caries: the BCS3-L1 strain

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Subash Chapagain
Subash Chapagain Sep 21, 2020
Dental caries (normally known as tooth decay) is the damage to a tooth when decay-causing bacteria in the mouth make acids that attack the tooth's surface, corroding the enamel. This can eventually lead to cavities in the tooth and if not treated properly can cause pain, infection and even loss of the tooth. Biofilm engineering is a novel approach in dental medicine that targets to replace/replenish the oral microbiota by providing cost-effective augmentation of conventional treatment strategies of oral health problems like caries. Hillman et. al. used this approach to construct an effector strain of oral microbial pathogen Streptococcus mutans that can be used for replacement therapy of dental caries. Note that Streptococcus mutans is the chief causative agent of dental caries. The effector strain, called BCS3-L1 was genetically engineered by using recombinant DNA technology to delete the gene encoding lactate dehydrogenase (ldh), rendering it incapable of producing lactic acid. To rectify for any possible metabolic imbalance due to ldh gene deletion, a supplemental alcohol dehydrogenase gene from Zymomonas mobilis was substituted in place of the deleted ldh gene (ldh ORF, basically). The resulting clone , BCS3-L1, produced virtually no detectable lactic acid when grown on different carbon sources. Total acid production was also significantly less due to increased ethanol and acetoin production. Additionally, the strain was also designed to synthesize a higher amount of a novel antibiotic peptide called mutacin 1140 providing a strong selective advantage over most other strains of Streptococcus mutans. In vitro and in vivo (rodent models), BCS3-L1 was genetically stable and showed no apparent negative side effects even during prolonged colonization. No gross or microscopic abnormalities of major organs were associated with oral colonization of rats with BCS3-L1 for 6 months. These primary results are indicative of the potential that even a single application of BCS3-L1 effector strain to human patients could result in permanent implantation, hence displacing over time the indigenous, caries causing S. mutans strains. References: 1.Hillman JD. Genetically modified Streptococcus mutans for the prevention of dental caries. Antonie Van Leeuwenhoek. 2002;82(1-4):361-366. 2. Hillman JD, Brooks TA, Michalek SM, Harmon CC, Snoep JL, van Der Weijden CC. Construction and characterization of an effector strain of Streptococcus mutans for replacement therapy of dental caries. Infect Immun. 2000;68(2):543-549. doi:10.1128/iai.68.2.543-549.2000
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Akkermansia Muciniphila

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Jamila
Jamila Sep 21, 2020
Centenarians have an abundance of certain bacteria in their gut microbiota these include verrucomicrobia, christensenellaceae, and bifidobacterium. Interestingly, a supplement containing Akkermansia muciniphila (belonging to the verrucomicrobia phylum) was able to increase the lifespan of mice with progeria in one study. [1] So the gut microbiota seems to be very important!! Reference 1. Bárcena, Clea, et al. "Healthspan and lifespan extension by fecal microbiota transplantation into progeroid mice." Nature medicine 25.8 (2019): 1234-1242.
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Darko Savic
Darko Savica year ago
Where could one find said Akkermansia? Asking for a friend:)
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Pseudomonas and Klebsiella spp.

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Shubhankar Kulkarni
Shubhankar Kulkarni Sep 21, 2020
- Pseudomonas and Klebsiella spp. - Human small intestine - These two groups of bacteria produce significant amounts of vitamin B12 (cyanocobalamin). Vitamin B12 is absorbed by the human gut. This is highly important since humans cannot synthesize vitamin B12. Gut microbiota and food are the only sources. There are other bacterial species that produce vitamin B12 but not as much as Pseudomonas and Klebsiella. Also, Bacteroidetes, Firmicutes, Actinobacteria, and Fusobacteria spp. also produce vitamin B12, but these bacteria reside in the human large intestine or the colon. Receptors that uptake vitamin B12 are present only in the small intestine. Pseudomonas and Klebsiella spp. are, therefore, important. References: 1. M J Albert, V I Mathan, S J Baker. Vitamin B12 synthesis by human small intestinal bacteria. Nature 1980 Feb 21;283(5749):781-2. doi: 10.1038/283781a0. 2. https://medium.com/microbial-instincts/vitamin-b12-can-gut-bacteria-synthesize-it-d64aa7b075da#:~:text=%E2%80%9CAlthough%20cobalamin%20%5Bvitamin%20B12%5D,bacteria%20can%20produce%20vitamin%20B12.
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Darko Savic
Darko Savica year ago
Great find! Which makes me think.. could we design our microbiome to supply us with all the essential micronutrients? If something currently cannot be secreted by a microbe, could we genetically modify a suitable species for this purpose?
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Darko Savic
Darko Savica year ago
Furthermore, a "designer microbiome" for a specific purpose - for example, species secreting nootropics, essential medications for specific diseases, etc:)
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Darko Savic
Darko Savica year ago
I was joking, but then this came up https://www.npr.org/templates/story/story.php?storyId=90014997&t=1600706282780
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Streptococcus oralis KJ3, Streptococcus uberis KJ2, and Streptococcus rattus JH145

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Darko Savic
Darko Savic Sep 21, 2020
Hillman developed ProBiora3, a probiotic that contains three bacterial strains: streptococcus oralis KJ3 streptococcus uberis KJ2 streptococcus rattus JH145 S. oralis and s. uberis both produce hydrogen peroxide; in vitro studies have shown that S. oralis and s. uberis are able to deplete pathogenic bacteria known to cause periodontal disease with the use of hydrogen peroxide. S. rattus JH145 is a lactate dehydrogenase deficient strain that is able to compete with s. mutans. Plaque derived from healthy sites is abundantly colonized with s. oralis and s. uberis. Whereas, plaque derived from diseased sites lacked s. oralis and s. uberis. References: As described in this session https://brainstorming.com/r/i7 Hillman, Jeffrey D., et al. "Safety assessment of ProBiora3, a probiotic mouthwash: subchronic toxicity study in rats." International journal of toxicology, 28.5, 2009, pp. 357-367. https://journals.sagepub.com/doi/full/10.1177/1091581809340705
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