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Nine core species have been identified that are highly consistent across UK, US, European, and non-western populations:
Five of the nine core microbes are also keystone species, indicating their central roles in the gut microbiome ecosystem in the Dutch population:
We identified 28 species and 53 pathways as potential keystone features, defined by more than 109 and 337 significant co-abundances, respectively.
Potential keystone species with low prevalence (≤10%) include:
These species are positively associated with multiple diseases, consistent with previous studies.
Huang et al. 2020 J. Med. Microbiol. 69: 797–805
The gut microbial patterns of the Xinjiang population include:
Most intestinal microbes are bacteria, which can be roughly divided into three categories:
The gut microbiome includes:
There are only a handful of known commensal strains that can potentially manipulate host physiological functions. A consortium of 11 bacterial strains isolated from healthy human donor feces is capable of robustly inducing interferon-gamma-producing Cytotoxic T cell (CTL) in the intestine:
Colonization of mice with this 11-strain mixture enhances both host resistance against Listeria monocytogenes infection and the therapeutic efficacy of immune checkpoint inhibitors in syngeneic tumor models. These strains act together to mediate the induction without causing inflammation, dependent on CD103+ dendritic cells (DC) and major histocompatibility (MHC) class Ia molecules. They primarily represent rare, low-abundance components of the human microbiome and have great potential as broadly effective biotherapeutics.
Lactobacillus, Streptococci, and Escherichia coli are found in small numbers in the gut. However, the human gut microbiota is dominated by four phyla:
Mokhtari et al. 2017 Adv Nutr 8(2): 240-252
The distinction between health-associated commensal bacteria and harmful pathogenic bacteria is not always clear, as some bacterial species can promote health or cause disease depending on the specific strain or their location in the body.
To effectively understand the ecology of the fecal microbiome, it is imperative to analyze both the rare and the abundant microbes. The diverse community of bacteria comprises a small number of abundant species plus a large number of rare or low-abundance species.
50% of total bacterial ribosomal RNA in cecal contents corresponds to Escherichia coli, enterococci, and Lactobacillus. However, Escherichia coli, enterococcus, and Lactobacillus account for only 7% of bacterial ribosomal RNA in fecal samples.
However, if these bacteria get out of balance (i.e., dysbiosis) it can lead to inflammation and health problems.
see also:
Bad Guys (certain harmful bacteria)
Composition & Gut microbiota
Diseases / Disorders & Gut microbiota
Good guys (certain beneficial bacteria)
Gut microbiota
Hermaphrodites
Human gut bacteria convert the secondary bile acid lithocholic acid with 3alfa-Hydroxysteroid Dehydrogenase into 3-Oxol-lithocholic acid (3-oxo LCA) as well as the abundant gut metabolite Isolithocholic acid (isoLCA))
Gut bacteria play a crucial role in maintaining the health of the gastrointestinal tract. They:
These activities help normalize the functioning of the gastrointestinal tract. However, gut dysbiosis - an imbalance in gut bacteria - can disrupt one or more of these parameters, leading to disturbances in normal gut function.
In addition:
Bacteria adapt to their local host genotype
Reference genomes for gut bacteria are underrepresented
It is estimated that <4% of the bacterial genomes in the US National Center for Biotechnology Information (NCBI) database belong to the human gut microbiota
The total density of bacteria is greater in the colon than the small intestine
Kim et al. 2017 Immunol Rev. 279(1): 90-105
It is more important to ask "what are the intestinal bacteria doing" than "which intestinal bacteria are there."
Less than 20% of All Gastrointestinal Bacteria Are Able to Be Cultured by Conventional Methodologies
see also:
Culturable Genome Reference (CGR)
Defending & Pathogens / Pathobionts / Pathogenic Bacteria
Gut microbiota
Host - Microbiota interactions