Creating an atlas to visualize the biodiversity of the mammalian gut microbiota.

Given the fundamental role played by the intestinal microbial community in influencing host health, it is not surprising that recent decades have been marked by increased efforts to determine the taxonomic composition of the human gut microbiota and its associated functions. Despite their generally accepted importance, these large-scale human-centered studies prevent an exhaustive overview of those mechanisms and factors that contribute to the mammalian gut microbiota assembly. However, Next-Generation Sequencing techniques and associated bioinformatic tools provide an exciting opportunity to rapidly expand our knowledge on the intestinal microbial communities associated with members of the Mammalia class. These non-human-focused studies established that dietary, host phylogeny, host physiology and anthropogenic influences represent the main factors driving the selection of a specific gut microbial consortium in mammals. The current review is aimed at providing a comprehensive overview on the impact that the above-mentioned factors exert on the assembly of the mammalian gut microbiota.

Metagenomic dissection of the canine gut microbiota: insights into taxonomic, metabolic and nutritional features.

Domestication of dogs from wolves is the oldest known example of ongoing animal selection, responsible for generating more than 300 dog breeds worldwide. In order to investigate the taxonomic and functional evolution of the canine gut microbiota, a multi-omics approach was applied to six wild wolves and 169 dog faecal samples, the latter encompassing 51 breeds, which fully covers currently known canine genetic biodiversity. Specifically, 16S rRNA gene and bifidobacterial Internally Transcribed Spacer (ITS) profiling were employed to reconstruct and then compare the canine core gut microbiota to those of wolves and humans, revealing that artificial selection and subsequent cohabitation of dogs with their owners influenced the microbial population of canine gut through loss and acquisition of specific bacterial taxa. Moreover, comparative analysis of the intestinal bacterial population of dogs fed on Bones and Raw Food (BARF) or commercial food (CF) diet, coupled with shotgun metagenomics, highlighted that both bacterial composition and metabolic repertoire of the canine gut microbiota have evolved to adapt to high-protein or high-carbohydrates intake. Altogether, these data indicate that artificial selection and domestication not only affected the canine genome, but also shaped extensively the bacterial population harboured by the canine gut.

Unveiling bifidobacterial biogeography across the mammalian branch of the tree of life.

Internally transcribed spacer (ITS) rRNA profiling is a novel tool for detailed analysis of microbial populations at low taxonomic ranks. Here we exploited this approach to explore species-level biogeography of the Bifidobacterium genus across 291 adult mammals. These include humans and 13 other primates, domesticated animals, such as dogs, cats, cows, sheep, goats, horses and pigs, and 46 additional species. The collected profiles revealed the presence of 89 putative novel bifidobacterial taxa in addition to 45 previously described species. Remarkably, in contrast to what is currently known for many gut commensals, we did not observe host-specialization among bifidobacterial species but rather their widespread distribution across mammals. Moreover, ITS rRNA profiling of wild relatives of domesticated dogs, rabbits and pigs clearly indicates that domestication and close contact with humans have impacted on the composition of the fecal bifidobacterial population. These data were complemented by analysis of bifidobacterial communities in milk of eight mammalian families, showing that bifidobacteria represent prototypical early gut microbiota members which are inherited by newborns from their lactating mother. Thus this study highlights the role of bifidobacteria as pioneering gut colonizers of a wide range of mammals.

Modulation of the Bifidobacterial Communities of the Dog Microbiota by Zeolite.

During last decades canine health and well being is becoming an important issue for human owners. In dogs, several factors including diet, pathogenic bacterial and stress conditions can affect the composition of the gut microbiota. In this study, we evaluated the effect of dietary chabazitic zeolitite (CZ) supplementation on the contribution of bifidobacteria to the fecal microbiota in training hunting dogs. Fecal microbiota cataloging based on 16S rRNA microbial profiling analyses highlighted an increase of Lactobacillus and Bifidobacterium in animals treated with CZ, with a simultaneous decrease of pathogens associated with dog gastrointestinal infections, such as Klebsiella and Enterobacter. A detailed profiling of the bifidobacterial population of dogs receiving CZ based on the ITS-based sequencing approach, revealed an enhancement bifidobacterial of species typical of animals such as Bifidobacterium animalis and B. pseudolongum. Moreover, these analyses identified the occurrence of putative new bifidobacterial taxa in both treated and untreated samples.

Exploring Amino Acid Auxotrophy in Bifidobacterium bifidum PRL2010.

The acquisition and assimilation strategies followed by members of the infant gut microbiota to retrieve nitrogen from the gut lumen are still largely unknown. In particular, no information on these metabolic processes is available regarding bifidobacteria, which are among the first microbial colonizers of the human intestine. Here, evaluation of amino acid auxotrophy and prototrophy of Bifidobacterium bifidum, with particular emphasis on B. bifidum strain PRL2010 (LMG S-28692), revealed a putative auxotrophy for cysteine. In addition, we hypothesized that cysteine plays a role in the oxidative stress response in B. bifidum. The use of glutathione as an alternative reduced sulfur compound did not alleviate cysteine auxotrophy of this strain, though it was shown to stimulate expression of the genes involved in cysteine biosynthesis, reminiscent of oxidative stress response. When PRL2010 was grown on a medium containing complex substrates, such as whey proteins or casein hydrolysate, we noticed a distinct growth-promoting effect of these compounds. Transcriptional analysis involving B. bifidum PRL2010 cultivated on whey proteins or casein hydrolysate revealed that the biosynthetic pathways for cysteine and methionine are modulated by the presence of casein hydrolysate. Such findings support the notion that certain complex substrates may act as potential prebiotics for bifidobacteria in their ecological niche.

Protective effects of proton pump inhibitors against indomethacin-induced lesions in the rat small intestine.

Proton pump inhibitors (PPIs) have been shown to be effective in preventing gastric and duodenal ulcers in high-risk patients taking nonsteroidal anti-inflammatory drugs (NSAIDs); by contrast, scarce information is available concerning the effects of PPIs on intestinal damage induced by NSAIDs in humans or in experimental animals. We examined the effects of lansoprazole and omeprazole on the intestinal injury induced by indomethacin in the conscious rat. PPIs were administered by the intragastric route at 30, 60 and 90 micromol/kg, 12 h and 30 min before and 6 h after indomethacin treatment. The effects of omeprazole and lansoprazole were evaluated on: (1) macroscopic and histologic damage; (2) mucosal polymorphonuclear cell infiltration; (3) oxidative tissue damage and (4) bacterial translocation from lumen into the intestinal mucosa. Lansoprazole and omeprazole (at 90 micromol/kg) significantly decreased (P<0.01) the macroscopic and histologic damage induced by indomethacin in the rat small intestine. Furthermore, both drugs greatly reduced (P<0.01) the associated increases in myeloperoxidase levels and lipid peroxidation induced by indomethacin, whereas they only moderately affected (P<0.05) the translocation of enterobacteria from lumen into the intestinal mucosa. These data demonstrate that omeprazole and lansoprazole can protect the small intestine from the damage induced by indomethacin in the conscious rat. The intestinal protection, possibly related to antioxidant and anti-inflammatory properties of these drugs, may suggest new therapeutic uses of PPIs in intestinal inflammatory diseases.