Phylum Dive: Firmicutes
Firmicutes is a one of the major phyla in the human gut, having the highest abundance of gut bacteria. The phylum consists of many beneficial bacteria but also some problematic bacteria at higher levels compared to the healthy cohort. For example, high levels of certain species of Firmicutes have been seen in patients with obesity, type II diabetes, and Irritable Bowel Syndrome. Other bacteria belonging to Firmicutes are major producers of short chain fatty acids that have many beneficial health implications: protection against Inflammatory Bowel Disease, diabetes, obesity, and cancer.
Firmicutes Keystone Species
Keystone species are bacteria that play crucial roles in the human gut, even though they aren’t necessarily seen at high abundances.
As seen above:
Bacillus spp. have been known to have antimicrobial properties making them beneficial to human health.
Eubacterium rectale is a butyrate producer. It also plays an important role in the fermentation of amino acids and uptake of sugars. Increasing your intake of fruits, vegetables and fibers can increase your Eubacterium rectale levels.
Faecalibacterium prausnitzii is the most abundant microbe in the human gut, and lower levels of Faecalibacterium prausnitzii compared to the healthy cohort have been noted in individuals with Crohn's Disease. Because Faecalibacterium prausnitzii can use many types of sugars and amino acids, it is able to produce short chain fatty acids such as butyrate, formate, and lactate. Faecalibacterium prausnitzii is important in maintaining homeostasis in the gut and works as an anti-inflammatory agent in mice.
Lactobacillus spp. are some of the biggest lactic acid producers; lactic acid aids in anti-microbial functions in the gut. Certain species also regulate cell death and assist the immune system. For example, Lactobacillus reuteri is used in probiotics and is helpful in killing harmful pathogens . However, compared to healthy cohorts, higher levels of Lactobacillus spp. have been seen in individuals with Autism Spectrum Disorder, but patients with Crohn's Disease show a lower abundance of beneficial Lactobacillus spp.
Roseburia spp. produce butyrate, propionate, and acetate through the fermentation of insoluble carbohydrates. They are overall a beneficial genus, with reduced levels in individuals with colorectal cancer and type II diabetes. Exercising and eating fruits, vegetables, and fibers can increase levels of Roseburia spp.
Ruminococcus spp. is a favorable genus with high abundances seen in healthy individuals. However, increased levels compared to healthy individuals have been noted in people with Irritable Bowel Syndrome. Lower abundances of Ruminococcus bromii have been seen in individuals who keep an animal-based diet; eating foods rich in fruits, vegetables, and fibers can increase levels of Ruminococcus bromii.
Works Cited:
Hasan, Nihal, and Hongyi Yang. “Factors Affecting the Composition of the Gut Microbiota, and Its Modulation.” PeerJ 7 (August 16, 2019): e7502. https://doi.org/10.7717/peerj.7502.
Jandhyala, Sai Manasa, Rupjyoti Talukdar, Chivkula Subramanyam, Harish Vuyyuru, Mitnala Sasikala, and D Nageshwar Reddy. “Role of the Normal Gut Microbiota.” World Journal of Gastroenterology : WJG 21, no. 29 (August 7, 2015): 8787–8803. https://doi.org/10.3748/wjg.v21.i29.8787.
Kagele, Dominique and Ph.D. “The ‘Skinny’ on Gut Microbes and Your Health.” The Jackson Laboratory. Accessed July 1, 2021. https://www.jax.org/news-and-insights/jax-blog/2015/may/the-skinny-on-gut-microbes-and-your-health.
Rajilić-Stojanović, Mirjana, and Willem M de Vos. “The First 1000 Cultured Species of the Human Gastrointestinal Microbiota.” Fems Microbiology Reviews 38, no. 5 (September 2014): 996–1047. https://doi.org/10.1111/1574-6976.12075.
Rinninella, Emanuele, Pauline Raoul, Marco Cintoni, Francesco Franceschi, Giacinto Abele Donato Miggiano, Antonio Gasbarrini, and Maria Cristina Mele. “What Is the Healthy Gut Microbiota Composition? A Changing Ecosystem across Age, Environment, Diet, and Diseases.” Microorganisms 7, no. 1 (January 10, 2019): 14. https://doi.org/10.3390/microorganisms7010014.
Welcome to the NirvanaBiome Blog
Welcome all microbe and microbiome lovers! We’ll try our best to keep you updated on recent developments in the field and science that’s related to microbes and the microbiome. Additionally, we would be really glad to make you smile through showing how fun, interesting, and accessible science can be in our blog. To launch our posts on microbes and the microbiome, we believe that theories on the emergence of life and our attempts to classify living organisms constitute great starting points. Therefore, our next 4 posts will give you some background on how the attempts to classify life initiated and how it led us to develop methods to characterize and classify microbes. We will then try to present different microbes and their relevance to humans and Earth. So, hold your seats, fasten your seatbelts and prepare to dive into the deepest roots of biology to start our journey into microbial life.
Theories on Emergence of Microscopic Life
It all begins with an idea.
The vast diversity of life on earth has fascinated humanity since antiquity and has driven us to develop numerous theories on the mechanisms generating diversity. Aristotle (384-322 BC) was the first person known to have a hot theory on how life diversified on earth: through spontaneous generation. Nonetheless, the invention of the microscope (1682) by Antonie von Leeuwenhoek delivered a blow to the observation of the spontaneous flourishing of life, including maggots, flies, vermin, fungi etc., from non-living things, such as rotten food, setting the framework for “Aristotelian Abiogenesis''. In 1859, the fade-in of microscopic living made Louis Pasteur test if the observation of “spontaneous generation” is due to microbes propagating in air. To test that, he boiled beef broth in an instrument of his invention that diffused air in and out but did not allow any microbial particles through. Pasteur’s boiled broth did not contain life, and confirmed the idea that diverse life on earth did not spontaneously arise from non-living things and implied that organisms arose from other organisms. Nonetheless, no one had a theory on where the microscopic life filtered out by Pasteur came from by the end of Pasteur’s experiment, not even Pasteur. By the mid 19th century, there was a gap in humanity’s understanding of how different microscopic living organisms emerged, yet bright people were already exploring ideas on the emergence of different macroscopic life either due to curiosity on human history and where humans came from or by sheer fascination by nature.
Figures 1-4 in the image show rabbit sperm and Fig. 5-8 show dog sperm observed by Leeuwenhoek (Image thanks to the permission of Wellcome Trust)
Tree of Life & Verge of Taxonomy
It all begins with an idea.
1859 was a golden year for biogenesis. Apart from Pasteur undermining “Spontaneous Generation”, Charles Darwin also published his groundbreaking book “On the Origin of Species”. The piece was successful at conceptualizing biogenesis into “Theory of Evolution”. According to evolutionary theory, the current diversity of life was generated by the living ancestors of the past. In the book, Darwin suggested that small variation in a species’ individuals’ distinguishing traits may be selected to diverge under different conditions. The divergence of traits may lead to the generation of new species or new groups of species (genus). Darwin illustrated the mode of life’s divergence as a branching tree of life (ToL) in his book.
This illustration of the branching tree of life which shows how life diversified, was the only illustration in The Origin of Species, Darwin, 1859
A classic example of natural selection’s capacity to shape different morphologies that also quite helped Darwin to establish his evolutionary theory came from Finches of Galapagos Islands during Darwin’s trip there. The morphological diversity of finches caused Darwin to not initially classify all finches that he collected during his trip as finches. Nevertheless, understanding that morphological differences of finches’ beaks were adaptations to different food sources on different Galapagos Islands led Darwin to think that all finches arose from a common ancestor that adapted to different food sources in different environments. The success of Darwin’s theory led other people to fizz with ideas to classify living organisms according to common morphological and behavioural traits or establishing novel ToLs. Classifying organisms according to common traits or similarities was an idea that was established by Carl Linnaeus in 1735, well before Darwin. Although the clades; animals, plants and minerals, where Linnaeus classified living are currently invalid, we still use the taxonomic ranking scale that he has once limited to kingdom, class, order, genus and species.
Darwin’s or Galapagos Finches, from The Voyage of Beagle, Darwin, 1845
Classification Rush
It all begins with an idea.
Darwin led lots of bright people to classify life based on their observable similarities and dissimilarities. Thanks to these attempts, numerous trees of life (ToLs) with different goals, ie. understanding the emergence of the human species or exploring major transitions in evolutionary history, were generated. 1879 was a significant year for microbial taxonomy, not just because Ernst Haeckal published another ToL putting humans to the very pinnacle of evolution, but also because he positioned microscopic amoeba to the root of ToL illustrating human evolution. Interestingly, Haeckal’s suggestion still appears true today since phylogenetic trees based on molecular techniques illustrate amoeba and animals diverging from a common ancestor. Haeckal’s ToL illustrates 2 kingdoms of the living: protists and animals. Following Haeckal’s ToL exploring microscopic organisms (Protists), Mereschkowski published another ToL suggesting that complex life forms such as animal and plants arose as a result of endosymbiosis of microscopic bacterial species, which in fact is partially correct. Today we know that eukaryotes arose as a result of an endosymbiosis between a bacterium and an archeon, and plants arose owing to an endosymbiosis between a eukaryote and a cholorophyllic bacterium thanks to developments in DNA-based molecular techniques. Hence, the lack of molecular techniques in 1905 may redeem Mereschkowski.
The ToL of Haeckal showing the evolution of human, The Evolution of Man, Haeckal, 1879
The ToL of Mereschkowski showing serial endosymbiosis that gave rise to eukaryotes and plants, Über Natur und Ursprung der Chromatophoren im Pflanzenreiche, Mereschkowski, 1905, Courtesy of Bill Martin
Nonetheless, Mereschowski neither knew what an archeon is nor that Archeae have stark similarities and dissimilarities to Bacteria. In 1925, Chatton realized that microscopic species had vast variation in their morphology and physiology, which suggested that classifying all microbes in the same domain is incorrect. Consequently, Chatton became the first to categorize all life into 2 domains, Eukaryota and Prokaryota, based on their nuclear morphology. After this division into two domains, inconsistencies due to morphology and physiology-based taxonomic attempts fueled later debates on how to branch these domains into kingdoms.
Molecular Revolution & Microbial Controversies
It all begins with an idea.
For 5 decades, Prokaryotes’ subdivision into Bacterial and Archaeal kingdoms remained unknown. Carl Woese became the first to resolve the taxonomic mystery thanks to developing 16s rRNA method classifying organisms based on sequence variation of the highly conserved and essential 16s rRNA gene. Significant divergence in prokaryotic 16s rRNA genes led Woese to divide the prokaryotic domain into archaeal and bacterial kingdoms which are also significantly divergent in physiology and ecology. Moreover, 16s rRNA method emerged to successfully assign taxa to eukaryotic organisms at a species resolution. The 16s method’s success in eukaryotic taxonomic identification, as well as prokaryotes’ subdivision into archaeal and bacterial kingdoms, led people to think about the branches of bacterial and archaeal domains into lower ranks of taxonomy, ie. phylum. Therefore, Woese attempted to identify the branch order of bacterial phyla using the 16s technique. Although the branch order of bacterial phyla is still debated, Woese’s attempt revealed that bacteria and archaea shared a common ancestor and archaea created a monophyletic group with eukaryotes. Consequently, Woese’s attempt to characterize bacterial phyla led him to divide 2 main domains (Prokaryote and Eukaryote, into 3 domains (Archaea, Bacteria and Eukarya).
Woese’s phlyogenetic ToL showing three domains of life, Towards a natural system of organisms: Proposal for the domains Archaea, Bacteria, and Eucarya, Woese et al. 1990
Woese’s successors tried to identify evolutionary bacterial phyla branches based on cell wall morphology, conserved coding mutations or conserved protein sequences. Yet, none was to have a verdict on the status of bacterial phyla branchings. Therefore, the scientific community welcomed a novel molecular method: whole-genome sequencing (WGS), to identify branchings in the lower ranks of bacterial taxonomy. WGS emerges as a more powerful technique as it compares and contrasts species’ whole genome sequences, instead of a single gene’s. Novel phylogenetic trees were also generated using WGS, but WGS arose new questions rather than resolving the issue on bacterial phyla branchings. WGS revealed that bacterial genes were interchangeable meaning that bacteria could transfer genes amongst themselves. Gene transfer amongst bacteria being common in nature, as well as some bacteria being unculturable,or cryptic in extreme environments further confounded how bacteria branched into lower phylum ranks of taxonomy. There is still an ongoing debate on bacterial phyla branching, as there is still also no common definition of what a bacterial species is. Understanding bacterial phyla branching order would resolve a mystery in evolutionary biology which may then focus our efforts on resolving bacterial taxonomy in finer ranks. To do that, it appears in order to understand what a bacterial phylum is and what is bacterial phyla’s ecological significance.