Metagenomic analysis reveals distinct patterns of gut lactobacillus prevalence, abundance, and geographical variation in health and disease

Abstract

Lactobacilli are exploited extensively for food fermentation and biotechnology. Some food and gut isolates have been developed as probiotics, for which species that may be commensal to the human host are considered desirable. However, the robustness of defining original niches for lactobacilli-food, environment, the gut-is questionable, and culture-independent analyses of prevalence in different human populations is lacking. Here we analyzed the abundance of lactobacilli in 6,154 subjects from a database of highly curated fecal shotgun metagenomics data spanning 25 nationalities, with ages ranging from infancy to 102 years. Twenty-five species were detected, which we assigned into low, medium, and high prevalence groups. The microbiome of apparently healthy individuals could be categorized into 6 clusters or Lactobacillotypes (LbTypes), with three of the Lbtypes being dominated by L. delbrueckii, L. ruminis, L. casei, and the other three comprising a combination of different species. These Lactobacillus clusters exhibit distinct global abundance patterns. The cluster prevalences also display distinct age-specific trends influenced by geography, with overall lactobacillus prevalence increasing significantly with age in North America and Europe but declining with age in non-Westernized societies. Regression analysis stratified by regional location identified distinct associations of the Lactobacillotypes with age, BMI, and gender. Cirrhosis, fatty-liver, , IBD and T2D were characterized by net gain of lactobacilli, whereas hypertension patients harbored depleted lactobacillus levels. Collectively these data indicate that the species abundance of gut lactobacilli is moderated by geography, diet, and interaction with the whole microbiome, and has strong interactions with diseases associated with a western lifestyle.

Maternal consumption of a fermented diet protects offspring against intestinal inflammation by regulating the gut microbiota

“…Lactobacillus has been widely studied because of its ability to enhance gut barrier function, balance the gut microbiota, modulate the innate immune system, and prevent the colonization of pathogenic bacteria, thereby benefiting host health. 36 Succiniclasticum can utilize succinate and produce propionate, thus providing benefits to gut health. 37 The results suggest that MFD not only inhibits pathogens but also plays an important role in the modulation of gut commensal microbiota.…”

Metabolomic Analysis of Lactobacillus acidophilus, L. gasseri, L. crispatus, and Lacticaseibacillus rhamnosus Strains in the Presence of Pomegranate Extract

“…Lactobacillus species are naturally found within human cavities, including the oral, gastrointestinal, and vaginal cavity. L. acidophilus, L. rhamnosus, L. gasseri , and L. crispatus species are found in all of these human environments (Klaenhammer et al, 2005 ; Selle and Klaenhammer, 2013 ; Ghosh et al, 2020 ). The four strains in this study were investigated to analyze two commonly used probiotics ( L. acidophilus NCFM and L. rhamnosus GG) and two potential probiotics ( L. crispatus NCK1351 and L. gasseri NCK1342) in combination with a polyphenolic substrate.…”

A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2

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