Centenarians have a unique microbiome that may protect them from certain bacterial infections

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Centenarians are less susceptible to age-related chronic diseases and more likely to survive infectious diseases.

Now, a new study reveals that people who live to be 100 or older have a unique microbiome that may protect them from certain bacterial infections including those caused by multidrug-resistant bacteria.

The findings, published in Nature, could help researchers develop new ways to treat chronic inflammation and bacterial disease.

A team of researchers including Yuko Sato, Koji Atarashi, Nobuoshi Hirose, and Kenya Honda at Keio University School of Medicine in Japan, and Damian Plichta and Ramnik Xavier at the Broad Institute of MIT and Harvard, studied microbes found in fecal samples from 160 Japanese centenarians who had an average age of 107.

They found that centenarians, compared to people aged 85 to 89 and those between 21 and 55, had higher levels of several bacterial species that produce molecules called secondary bile acids.

Secondary bile acids are generated by microbes in the colon and are thought to help protect the intestines from pathogens and regulate the body’s immune responses.

The researchers next treated common infection-causing bacteria in the lab with the secondary bile acids that were elevated in the centenarians. One molecule, called isoalloLCA, strongly inhibited the growth of Clostridioides difficile, an antibiotic-resistant bacterium that causes severe diarrhea and gut inflammation. Feeding mice infected with C. difficile diets supplemented with isoalloLCA similarly suppressed levels of the pathogen.

The team also found that isoalloLCA potently inhibited the growth of or killed many other gram positive pathogens, suggesting that isoalloLCA may help the body maintain the delicate equilibrium of microbial communities in a healthy gut.

“The ecological interaction between the host and different processes in bacteria really suggests the potential of these gut bugs for health maintenance,” said Plichta, a computational scientist at the Broad and co-first author of the study.

Larger and longer-term studies from different regions around the world may help uncover a causal link between longevity and bile acids. In the meantime, the bacteria identified in this study could help researchers study how to manipulate bile acids to treat infections caused by antibiotic-resistant bacteria.

“A unique cohort, international collaboration, computational analysis, and experimental microbiology all enabled this discovery that the gut microbiome holds the keys to healthy aging,” said Xavier, core institute member at the Broad and co-corresponding author of the study.

“Our collaborative work shows that future studies focusing on microbial enzymes and metabolites can potentially help us identify starting points for therapeutics.”


The mammalian gut is a unique organ that harbors trillions of commensal bacteria (Sender et al., 2016) as well as a large number of immune cells that are segregated from the resident microbiota by a single layer of epithelial cells. The close proximity of microbial and host cells creates a challenge for the gut-residing immune cells, which must protect the host against harmful pathogens while maintaining tolerance to commensal microbes (Whibley et al., 2019).

While it is known that immune cells shape the composition of gut microbiota (Pandiyan et al., 2019), a growing number of studies now indicate that gut microbes regulate the development and function of host immune cells. Furthermore, these studies incidate that alterations in the gut microbial community can lead to pathological conditions including disrupted barrier function and heightened intestinal inflammation (Lloyd-Price et al., 2019; Michail et al., 2012; Munoz et al., 2019).

Regulatory T (Treg) cells are a subset of CD4+ T helper cells that are abundant in the gut lamina propria. The transcription factor forkhead box P3 (FOXP3) promotes the differentiation of Treg cells (Fontenot et al., 2003; Hori et al., 2003), which play a critical role in promoting gut immune homeostasis (Sakaguchi et al., 2008).

The abnormal regulation of these cells is closely associated with autoimmune and inflammatory diseases including colitis (Maul et al., 2005; Sakaguchi, 2005). Evidence indicates that Treg cells are regulated by the gut microbiota, suggesting that gut bacteria can directly influence adaptive immunity (Arpaia et al., 2013; Furusawa et al., 2013; Mazmanian et al., 2008).

Indeed, both commensal strains (Atarashi et al., 2013; Sefik et al., 2015) and bacterially derived metabolites such as short-chain fatty acids (Arpaia et al., 2013; Smith et al., 2013) and polysaccharide A (Mazmanian et al., 2008) have been shown to modulate Treg differentiation.

Secondary bile acids are another group of bacterial metabolites that function as T cell modulators. Primary bile acids are steroidal compounds that are synthesized from cholesterol in the liver and secreted into the gut lumen after a meal, where they facilitate uptake of dietary fatty acids and vitamins (Ridlon et al., 2006).

Once these compounds reach the lower gastrointestinal (GI) tract, they are chemically modified by the resident microbiota to form a class of metabolites called secondary bile acids (Ridlon et al., 2006). A growing body of evidence indicates that both primary and secondary bile acids affect host physiology, including metabolism and immune response (Fiorucci and Distrutti, 2015; Pols et al., 2017; Song et al., 2020; Thomas et al., 2008; Vavassori et al., 2009).

Indeed, prior work has demonstrated that either groups of bile acids or the specific secondary bile acids modulate the function and differentiation of Treg cells (Campbell et al., 2020; Hang et al., 2019; Song et al., 2020). For example, we recently demonstrated that the bile acid metabolite isoallolithocholic acid (isoalloLCA), an isomer of the secondary bile acid lithocholic acid (LCA), enhances the differentiation of naïve T cells into Treg cells both in vitro and in vivo (Hang et al., 2019).

LCA is one of the most abundant secondary bile acids, with mean concentrations of ∼160 μM in human cecal contents (Hamilton et al., 2007). While LCA is exclusively produced by gut bacteria (Ridlon et al., 2006), the biosynthetic pathway for the production of the isomeric compound isoalloLCA is unknown.

This bile acid is absent from germ-free B6 mice (Hang et al., 2019), indicating that a microbiome is necessary for the production of this immunomodulatory metabolite and suggesting that gut bacteria may play a direct role in the synthesis of this compound.

Moreover, the way in which isoalloLCA enhances Treg cell differentiation is not fully understood. The Treg cell-modulating activity of isoalloLCA was found to depend on an enhancer of the Foxp3 gene, the conserved noncoding sequence (CNS) 3 (Hang et al., 2019). This mechanism is unique amongst small molecules that promote Treg differentiation.

The bacterial metabolites butyrate and isodeoxycholic acid (isoDCA) increase Foxp3 gene expression and Treg cell differentiation in a CNS1-dependent manner (Arpaia et al., 2013; Campbell et al., 2020). While our previous work indicated that isoalloLCA increases H3K27 acetylation at the Foxp3 promoter region, the host factor directly responsible for isoalloLCA-dependent upregulation of Foxp3 gene expression is unknown.

In this work, we sought to determine whether human gut bacteria can biosynthesize isoalloLCA and to elucidate the mechanism by which isoalloLCA enhances Treg cell differentiation. Here, we identify species of Bacteroidetes, a phylum of bacteria that is abundant in the human gut, that produce isoalloLCA.

Producer strains possess an inducible operon required for isoalloLCA synthesis in vitro and in vivo in germ-free (GF) mice monocolonized with Bacteroidetes species. We also demonstrate that isoalloLCA induces the differentiation of naïve T cells to Treg cells through the nuclear hormone receptor NR4A1.

IsoalloLCA treatments result in the increased binding of NR4A1 at the Foxp3 locus, leading to enhanced Foxp3 gene transcription. Notably, both the levels of isoalloLCA and the abundance of isoalloLCA-producing bacterial genes are significantly reduced in human inflammatory bowel disease (IBD) cohorts compared to healthy controls. This study reveals a mechanism by which commensal bacteria regulate immune tolerance in the gut and suggests that isoalloLCA and the bacteria that produce this bile acid may temper inflammatory responses in the human GI tract.

reference link:https://www.biorxiv.org/content/10.1101/2021.01.08.425963v1.full


More information: Yuko Sato et al, Novel bile acid biosynthetic pathways are enriched in the microbiome of centenarians, Nature (2021). DOI: 10.1038/s41586-021-03832-5

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