Libanicoccus massiliensis gen. nov., sp. nov., a new bacterium isolated from human stool

Urbanization associates with restricted gut microbiome diversity and delayed maturation in infants

Alterations of the microbiome are linked to increasingly common diseases such as obesity, allergy, and inflammatory bowel disease. Post-industrial lifestyles are thought to contribute to the gut microbiome alterations that cause or aggravate these diseases. Comparing communities across the industrialization spectrum can reveal associations between gut microbiome alterations and lifestyle and health, and help pinpoint which specific aspect of the post-industrial lifestyle is linked to microbiome alterations. Here, we compare the gut microbiomes of 60 mother and infant pairs from rural and urban areas of Senegal over two time points. We find that urban mothers, who were more frequently overweight, had different gut microbiome compositions than rural mothers, showing an expansion of Lachnospiraceae and Enterobacter. Urban infants, on the other hand, showed a delayed gut microbiome maturation and a higher susceptibility to infectious diseases. Thus, we identify new microbiome features associated with industrialization, whose association with disease may be further investigated.

Identification of intestinal and fecal microbial biomarkers using a porcine social stress model

Understanding the relationships between social stress and the gastrointestinal microbiota, and how they influence host health and performance is expected to have many scientific and commercial implementations in different species, including identification and improvement of challenges to animal welfare and health. In particular, the study of the stress impact on the gastrointestinal microbiota of pigs may be of interest as a model for human health. A porcine stress model based on repeated regrouping and reduced space allowance during the last 4 weeks of the finishing period was developed to identify stress-induced changes in the gut microbiome composition. The application of the porcine stress model resulted in a significant increase in salivary cortisol concentration over the course of the trial and decreased growth performance and appetite. The applied social stress resulted in 32 bacteria being either enriched (13) or depleted (19) in the intestine and feces. Fecal samples showed a greater number of microbial genera influenced by stress than caecum or colon samples. Our trial revealed that the opportunistic pathogens Treponema and Clostridium were enriched in colonic and fecal samples from stressed pigs. Additionally, genera such as Streptococcus, Parabacteroides, Desulfovibrio, Terrisporobacter, Marvinbryantia, and Romboutsia were found to be enriched in response to social stress. In contrast, the genera Prevotella, Faecalibacterium, Butyricicoccus, Dialister, Alloprevotella, Megasphaera, and Mitsuokella were depleted. These depleted bacteria are of great interest because they synthesize metabolites [e.g., short-chain fatty acids (SCFA), in particular, butyrate] showing beneficial health benefits due to inhibitory effects on pathogenic bacteria in different animal species. Of particular interest are Dialister and Faecalibacterium, as their depletion was identified in a human study to be associated with inferior quality of life and depression. We also revealed that some pigs were more susceptible to pathogens as indicated by large enrichments of opportunistic pathogens of Clostridium, Treponema, Streptococcus and Campylobacter. Generally, our results provide further evidence for the microbiota-gut-brain axis as indicated by an increase in cortisol concentration due to social stress regulated by the hypothalamic-pituitary-adrenal axis, and a change in microbiota composition, particularly of bacteria known to be associated with pathogenicity and mental health diseases.

Multi-Omics Analysis Reveals Age-Related Microbial and Metabolite Alterations in Non-Human Primates

Aging is a systemic physiological degenerative process, with alterations in gut microbiota and host metabolism. However, due to the interference of multiple confounding factors, aging-associated molecular characteristics have not been elucidated completely. Therefore, based on 16S ribosomal RNA (rRNA) gene sequencing and non-targeted metabolomic detection, our study systematically analyzed the composition and function of the gut microbiome, serum, and fecal metabolome of 36 male rhesus monkeys spanning from 3 to 26 years old, which completely covers juvenile, adult, and old stages. We observed significant correlations between 41 gut genera and age. Moreover, 86 fecal and 49 serum metabolites exhibited significant age-related correlations, primarily categorized into lipids and lipid-like molecules, organic oxygen compounds, organic acids and derivatives, and organoheterocyclic compounds. Further results suggested that aging is associated with significant downregulation of various amino acids constituting proteins, elevation of lipids, particularly saturated fatty acids, and steroids. Additionally, age-dependent changes were observed in multiple immune-regulatory molecules, antioxidant stress metabolites, and neurotransmitters. Notably, multiple age-dependent genera showed strong correlations in these changes. Together, our results provided new evidence for changing characteristics of gut microbes and host metabolism during aging. However, more research is needed in the future to verify our findings.

Unique Pakistani gut microbiota highlights population-specific microbiota signatures of type 2 diabetes mellitus

Biogeographic variations in the gut microbiota are pivotal to understanding the global pattern of host-microbiota interactions in prevalent lifestyle-related diseases. Pakistani adults, having an exceptionally high prevalence of type 2 diabetes mellitus (T2D), are one of the most understudied populations in microbiota research to date. The aim of the present study is to examine the gut microbiota across individuals from Pakistan and other populations of non-industrialized and industrialized lifestyles with a focus on T2D. The fecal samples from 94 urban-dwelling Pakistani adults with and without T2D were profiled by bacterial 16S ribosomal RNA gene and fungal internal transcribed spacer (ITS) region amplicon sequencing and eubacterial qPCR, and plasma samples quantified for circulating levels of lipopolysaccharide-binding protein (LBP) and the activation ability of Toll-like receptor (TLR)-signaling. Publicly available datasets generated with comparable molecular methods were retrieved for comparative analysis of the bacterial microbiota. Overall, urbanized Pakistanis' gut microbiota was similar to that of transitional or non-industrialized populations, depleted in Akkermansiaceae and enriched in Prevotellaceae (dominated by the non-Westernized clades of Prevotella copri). The relatively high proportion of Atopobiaceae appeared to be a unique characteristic of the Pakistani gut microbiota. The Pakistanis with T2D had elevated levels of LBP and TLR-signaling in circulation as well as gut microbial signatures atypical of other populations, e.g., increased relative abundance of Libanicoccus/Parolsenella, limiting the inter-population extrapolation of gut microbiota-based classifiers for T2D. Taken together, our findings call for a more global representation of understudied populations to extend the applicability of microbiota-based diagnostics and therapeutics.

Granulimonas faecalis gen. nov., sp. nov., and Leptogranulimonas caecicola gen. nov., sp. nov., novel lactate-producing Atopobiaceae bacteria isolated from mouse intestines, and an emended description of the family Atopobiaceae

Two strictly anaerobic, Gram-stain-positive, non-motile bacteria (strains OPF53T and TOC12T) were isolated from mouse intestines. Strains OPF53T and TOC12T grew at pH 5.5–9.0 and 5.0–9.0, respectively, and at temperatures of 30–45 °C. The cell morphologies of these strains were short rods and rods, respectively, and the cells possessed intracellular granules. The major cellular fatty acids of OPF53T were C18  :  1 cis 9 and C18  :  1 cis 9 dimethyl acetal, whereas those of TOC12T were C18  :  0 and C18  :  1 cis 9. In OPF53T, the main end-products of modified peptone–yeast extract–glucose (PYG) fermentation were lactate, formate and butyrate, whereas, in addition to these acids, TOC12T also produced hydrogen. The genomes of OPF53T and TOC12T were respectively 2.2 and 2.0 Mbp in size with a DNA G+C contents of 69.1 and 58.7 %. The 16S rRNA gene sequences of OPF53T and TOC12T showed the highest similarity to members of the family Atopobiaceae , namely, Olsenella phocaeensis Marseille-P2936T (94.3 %) and Olsenella umbonata KCTC 15140T (93.2 %), respectively. Phylogenetic analyses revealed that both isolates formed distinct lineages from other genera of the family Atopobiaceae . In addition, the two strains were characterized by relatively low 16S rRNA gene sequence similarity (93.4 %) and can be distinguished by their distinctive traits (including cell shape, DNA G+C content, and major fatty acids profiles). On the basis of their polyphasic taxonomic properties, these isolates represent two noel species of two novel genera within the family Atopobiaceae , for which the names Granulimonas faecalis gen. nov., sp. nov. (OPF53T=JCM 35015T=KCTC 25474T) and Leptogranulimonas caecicola gen. nov., sp. nov. (TOC12T=JCM 35017T=KCTC 25472T) are proposed.

Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019

Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.

Comparative genomics of Parolsenella catena and Libanicoccus massiliensis: Reclassification of Libanicoccus massiliensis as Parolsenella massiliensis comb. nov

Previous analyses based on 16S rRNA and hsp60 genes indicated that Parolsenella catena and Libanicoccus massiliensis were closely related to each other and formed a monophyletic cluster independent of the related Olsenella species. To clarify the relationship of these two species, we determined the genome sequence of P. catena JCM 31932T and compared it with that already sequenced for L. massiliensis Marseille-P3237T. Phylogenetic trees based on the concatenated 37 single-copy ribosomal proteins or RpoB robustly supported the relationship observed in the previous studies. Digital DNA–DNA hybridization and average nucleotide identity (ANI) values between P. catena JCM 31932T and L. massiliensis Marseille-P3237T were 32.6 and 87.8 %, respectively, indicating that P. catena JCM 31932T and L. massiliensis Marseille-P3237T are independent species. Alignment fraction and ANI values between the two genomes were 0.75 and 88.84 %, respectively, thus indicating that the two species should be classified into the same genus. The number of putative orthologous genes shared between the two genomes was 1321, which was significantly larger than those (482–928) reported between L. massiliensis Marseille-P3237T and other closely related species. In addition, the genome of P. catena JCM 31932T had a high degree of synteny conservation with that of L. massiliensis Marseille-P3237T. On the basis of these findings, we propose that L. massiliensis should be reclassified as Parolsenella massiliensis comb. nov.; the type strain is Marseille-P3237T (=JCM 33000T=CCUG 71182T).

Miniphocibacter massiliensis gen. nov., sp. nov., a new species isolated from the human gut and its taxono-genomics description

With the aim of describing the human microbiota by the means of culture methods, culturomics was developed in order to target previously un‐isolated bacterial species and describe it via the taxono‐genomics approach. While performing a descriptive study of the human gut microbiota of the pygmy people, strain Marseille‐P4678^T has been isolated from a stool sample of a healthy 39‐year‐old pygmy male. Cells of this strain were Gram‐positive cocci, spore‐forming, non‐motile, catalase‐positive and oxidase‐negative, and grow optimally at 37°C under anaerobic conditions. Its 16S rRNA gene sequence exhibited 89.69% of sequence similarity with Parvimonas micra strain 3119B^T (NR 036934.1), its phylogenetically closest species with standing in nomenclature. The genome of strain Marseille‐P4678^T is 2,083,161 long with 28.26 mol% of G+C content. Based on its phenotypic, biochemical, genotypic and proteomic profile, this bacterium was classified as a new bacterial genus and species Miniphocibacter massiliensis gen. nov., sp. nov. with the type strain Marseille‐P4678^T.