Ecology impacts the decrease of Spirochaetes and Prevotella in the fecal gut microbiota of urban humans

Abstract

Compared to the huge microbial diversity in most mammals, human gut microbiomes have lost diversity while becoming specialized for animal-based diets – especially compared to chimps, their genetically closest ancestors. The lowered microbial diversity within the gut of westernized populations has also been associated with different kinds of chronic inflammatory diseases in humans. To further deepen our knowledge on phylogenetic and ecologic impacts on human health and fitness, we established the herein presented biobank as well as its comprehensive microbiota analysis. In total, 368 stool samples from 38 different animal species, including Homo sapiens, belonging to four diverse mammalian orders were collected at seven different locations and analyzed by 16S rRNA gene amplicon sequencing. Comprehensive data analysis was performed to (i) determine the overall impact of host phylogeny vs. diet, location, and ecology and to (ii) examine the general pattern of fecal bacterial diversity across captive mammals and humans.By using a controlled study design with captive mammals we could verify that host phylogeny is the most dominant driver of mammalian gut microbiota composition. However, the effect of ecology appears to be able to overcome host phylogeny and should therefore be studied in more detail in future studies. Most importantly, our study could observe a remarkable decrease of Spirochaetes and Prevotella in westernized humans and platyrrhines, which is probably not only due to diet, but also to the social behavior and structure in these communities.Our study highlights the importance of phylogenetic relationship and ecology within the evolution of mammalian fecal microbiota composition. Particularly, the observed decrease of Spirochaetes and Prevotella in westernized communities might be associated to lifestyle dependent rapid evolutionary changes, potentially involved in the establishment of dysbiotic microbiomes, which promote the etiology of chronic diseases.

Lacticaseibacillus rhamnosus-Derived Exopolysaccharide Attenuates D-Galactose-Induced Oxidative Stress and Inflammatory Brain Injury and Modulates Gut Microbiota in a Mouse Model

“…The abundance of Proteobacteria has been reported as a potential diagnostic marker for dysbiosis and other metabolic diseases [ 56 ]. Spirochaetes have been reported to degrade polymers like xylan, pectin arabinogalactan, and hemicellulose and have also been known to synthesize short-chain fatty acids from plant polysaccharides [ 57 , 58 ]. Based on the above inference, Spirochaetes may utilize EPSRam12 and Beta-glucan, resulting in an increase in the proportion of Spirochaetes in the EPS and Beta-glucan group.…”

Anthropogenic Disturbance Impacts Gut Microbiome Homeostasis in a Malagasy Primate

“…Furthermore, the lower abundance of these phyla makes the host susceptible to other gut disturbances ( Kalkeri et al, 2021 ). Spirochaetes are normally present in the gut microbiomes of humans and other mammals and play an important role in the digestion of plant polysaccharides ( Thingholm et al, 2021 ). Moreover, in baboons, social interactions are crucial for the transmission of gut bacteria, specifically anaerobic and non-spore-forming bacteria such as Spirochaetes, between members of the same social group ( Tung et al, 2015 ).…”

Application of a multispecies probiotic reduces gastro-intestinal discomfort and induces microbial changes after colonoscopy

“…Total DNA was isolated at the Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany according to published procedures (35). Briefly, the QIAamp DNA fast stool mini kit automated on the QIAcube (Qiagen, Hilden, Germany) was used for DNA extraction according to manufacturer’s instructions.…”

“…Briefly, the QIAamp DNA fast stool mini kit automated on the QIAcube (Qiagen, Hilden, Germany) was used for DNA extraction according to manufacturer’s instructions. For mechanic lysis, sample were bead beating using the 0.70 mm Garnet Bead tubes (Dianova, Hamburg, Germany) filled with 1.1 ml InhibitEx lysis buffer in a SpeedMill PLUS (Analytik Jena, Jena, Germany) for 45s at 50Hz according to manufacturer’s instructions and as published (35). Isolated nucleic acids were stored at -20°C until further processing.…”

“…Paired-end sequencing data were received as FASTQ files from the microbiome lab at the Christian-Albrechts-University Kiel according to published procedures (36). Briefly, amplification of the 16S rRNA gene was performed, targeting the hypervariable regions V1-V2 with the target specific primers 27F (5'-AGA GTT TGA TCC TGG CTC AG-3') and 338R (5'-GCT GCC TCC CGT AGG AGT-3').…”