Blautia argi sp. nov., a new anaerobic bacterium isolated from dog faeces

Age and aging process alter the gut microbes

BACKGROUND

Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE

To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS

Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS

The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS

The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.

Aerococcus kribbianus sp. nov., a facultatively anaerobic bacterium isolated from pig faeces

Two cocci-shaped, facultatively anaerobic, Gram-positive bacteria isolated from the faeces of a pig were designated as strains YH-aer221T and YH-aer222. Analysis of the 16S rRNA gene sequences revealed that the isolates were most closely related to Aerococcus suis JCM 18035T with 96.6 % similarity. The multi-locus sequence tree revealed that the isolates formed a sub-cluster adjacent to A. suis JCM 18035T. The average nucleotide identity values for the isolates and their most closely related strains were 71.8 and 71.7 %, respectively; and the digital DNA-DNA hybridization values for the isolates and their most closely related strains were 25.6 and 25.5 %, respectively. The main fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 0. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The two isolates shared the same metabolic pathways. Isolates YH-aer221T and YH-aer222 harboured the same CRISPR array with 33 and 46 spacers, respectively. Single-genome vs. metagenome analysis showed that the genomes of the isolates were not found in the available metagenome database. Given their chemotaxonomic, phenotypic and phylogenetic properties, YH-aer221T (= KCTC 25571T=JCM 35699T) and YH-aer222 (=KCTC 25573=JCM 35700) represent a novel taxon. The name Aerococcus kribbianus sp. nov. is proposed.

Changes in the Gut Microbiota Composition during Implantation of Composite Scaffolds Based on Poly(3-hydroxybutyrate) and Alginate on the Large-Intestine Wall

The development of biopolymer scaffolds for intestine regeneration is one of the most actively developing areas in tissue engineering. However, intestinal regenerative processes after scaffold implantation depend on the activity of the intestinal microbial community that is in close symbiosis with intestinal epithelial cells. In this work, we study the impact of different scaffolds based on biocompatible poly(3-hydroxybutyrate) (PHB) and alginate (ALG) as well as PHB/ALG scaffolds seeded with probiotic bacteria on the composition of gut microbiota of Wistar rats. Implantation of PHB/ALG scaffolds on the large-intestine wall to close its injury showed that alpha diversity of the gut microbiota was not reduced in rats implanted with different PHB/ALG scaffolds except for the PHB/ALG scaffolds with the inclusion of Lactobacillus spheres (PHB/ALG-L). The composition of the gut microbiota of rats implanted with PHB/ALG scaffolds with probiotic bacteria or in simultaneous use of an antimicrobial agent (PHB/ALG-AB) differed significantly from other experimental groups. All rats with implanted scaffolds demonstrated shifts in the composition of the gut microbiota by individual operational taxonomic units. The PHB/ALG-AB construct led to increased abundance of butyrate-producing bacteria: Ileibacterium sp. dominated in rats with implanted PHB/ALG-L and Lactobacillus sp. and Bifidobacterium sp. dominated in the control group. In addition, the PHB/ALG scaffolds had a favourable effect on the growth of commensal bacteria. Thus, the effect of implantation of the PHB/ALG scaffold compared to other scaffolds on the composition of the gut microbiota was closest to the control variant, which may demonstrate the biocompatibility of this device with the microbiota.

Description and comparative genome analysis of Hallella absiana sp. nov., isolated from pig feces

OBJECTIVE

The genus Hallella was described within Bacteroidaceae, and then reclassified within Prevotellaceae based on its phenotypic and phylogenetic description. It is associated with degradation of carbohydrate. However, some species of Hallella have pathobiotic properties, and are involved in infections and chronic inflammatory disorders.

METHODS

Here, we used a polyphasic taxonomic approach to characterize the two strains: YH-C38^T and YH-C4B9b. A detailed metabolic analysis was conducted to compare the two novel isolates with related strains within the genus Hallella.

RESULT

Analysis of 16S rRNA gene sequences revealed that the isolates were most closely related to Hallella mizrahii JCM 34422^T with 98.5% and 98.6% similarities, respectively. Analysis of the multi-locus species tree based on whole genome sequences of the isolates and related strains revealed that the isolates formed a sub-cluster adjacent to H. mizrahii JCM 34422^T. The average nucleotide identity values for YH-C38^T and YH-C4B9b, and the most closely related strain H. mizrahii JCM 34422^T, were 93.5% and 93.8%, respectively. The main fatty acids were iso C_17:0 3OH and anteiso C_15:0. The predominant menaquinones were MK-12, MK-11, and MK-13. The cell wall contained the peptidoglycan of meso-diaminopimelic acid. Analysis of comparative metabolic analysis revealed that isolates YH-C38^T and YH-C4B9b each contained 155 carbohydrate-active enzymes, and glycoside hydrolase was the largest family.

CONCLUSION

Two rod-shaped, obligately anaerobic, Gram-stain-negative bacteria, isolated from pig feces, were designated as strains YH-C38^T and YH-C4B9b. Based on the chemotaxonomic, phenotypic, and phylogenetic properties, YH-C38^T (=KCTC 25103^T = JCM 35423^T) and YH-C4B9b (=KCTC 25104 = JCM 35609) represent a novel taxon. The name Hallella absiana sp. nov. is proposed.

An Update on Novel Taxa and Revised Taxonomic Status of Bacteria Isolated from Domestic Animals Described in 2018 to 2021

Novel bacterial taxonomy and nomenclature revisions can have significant impacts on clinical practice, disease epidemiology, and veterinary microbiology laboratory operations. Expansion of research on the microbiota of humans, animals, and insects has significant potential impacts on the taxonomy of organisms of clinical interest. Implications of taxonomic changes may be especially important when considering zoonotic diseases. Here, we address novel taxonomy and nomenclature revisions of veterinary significance. Noteworthy discussion centers around descriptions of novel mastitis pathogens in Streptococcaceae, Staphylococcaceae, and Actinomycetaceae; bovine reproductive tract pathogens in Corynebacteriaceae; novel members of Mannheimia spp., Leptospira spp., and Mycobacterium spp.; the transfer of Ochrobactrum spp. to Brucella spp.; and revisions to the genus Mycoplasma.

Profiling Blautia at high taxonomic resolution reveals correlations with cognitive dysfunction in Chinese children with Down syndrome

Introduction

Down syndrome (DS), the presence of a supernumerary chromosome 21, is associated with cognitive dysfunction caused by early neurodegenerative processes. Alterations in the gut microbiota were observed in Chinese children with DS, and the genus Blautia was associated with cognitive function in these children. Therefore, it is crucial to understand the detailed composition of this group at the species level and to explore the effect of specific species on cognitive function.

Methods

In this study, Blautia-specific amplicon sequencing was conducted to identify the specific Blautia species in 15 children with DS and 15 matched healthy children.

Results

The taxonomic analyses suggested that the Blautia taxa were clustered by disease status. The diversity of Blautia at the species level differed between DS patients and healthy controls, with the abundances of Blautia massiliensis and Blautia argi decreasing in DS children, while Blautia faecis was increased. Acetic acid, one of the metabolites of Blautia, was significantly reduced in the DS group. Of particular interest, Kyoto Encyclopaedia of Genes and Genomes analysis revealed decreased modules related to starch and sucrose metabolism and glycolysis. In addition, B. argi was positively related to DS cognitive scores, and B. faecis was negatively related to cognitive function, implying its role on the DS cognitive impairments.

Discussion

Our study has important implications for understanding the important effects of specific species of Blautia on cognitive function and thus possibly provides a new strategy for future studies of cognitive improvement in individuals with DS.

Effect of rumen microbiota transfaunation on the growth, rumen fermentation, and microbial community of early separated Japanese Black cattle

This study aimed to investigate the effect of rumen microbiota transfaunation on the growth, rumen fermentation, and the microbial community of Japanese Black cattle that were separated early from their dams. Here, 24 calves were separated from their dams immediately after calving, 12 of which were transfaunated via inoculation with rumen fluid from adult cattle at the age of 2 months while the remaining 12 were kept unfaunated (not-inoculated). Feed efficiency monitoring was performed during 7-10 months of age. Body weight and feed intake were not significantly different between the transfaunated and unfaunated cattle. Transfaunation increased the relative levels of acetate and butyrate but decreased those of propionate, which increased the non-glucogenic/glucogenic short-chain fatty acid ratio. Microbial 16S, 18S, and ITS ribosomal RNA gene amplicon analysis showed that rumen microbial diversity and composition differed between transfaunated and unfaunated cattle; transfaunation increased the abundance of acetate- and butyrate-producing bacteria, and decreased the abundance of bacterial genera associated with propionate production. Transfaunation also increased the abundance of Methanomassiliicoccaceae_group10 (1.94% vs. 0.05%) and Neocallimastix (27.1% vs. 6.8%) but decreased that of Methanomicrobium (<0.01% vs. 0.06%). Our findings indicate that rumen microbiota transfaunation shifts rumen fermentation toward acetate and butyrate production through a change in the rumen microbial composition in Japanese Black cattle.

Lacticaseibacillus kribbianus sp. nov., isolated from pig farm faeces dump

A lactic acid bacteria isolated from pig faeces was characterized using a polyphasic approach. Cells of the strain were Gram-stain-positive, rod-shaped and facultative anaerobic. Phylogenetic analysis of 16S rRNA gene sequence indicated that the isolate belonged to the genus Lacticaseibacillus; however, the similarity to other homologues within the genus was <98 %. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster adjacent to Lacticaseibacillus absianus and Lacticaseibacillus daqingensis. The main fatty acids of the strain is the C_18 : 1ω9c and C_16 : 0. The G+C content of the genomic DNA was 62.8 mol %. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, aminophospholipids and phospholipids. The cell-wall peptidoglycan did not contain meso-diaminopimelic acid. Thus, YH-lac21^T (=KCTC 21185=JCM 34953) represents a novel species. The name Lacticaseibacillus kribbianus sp. nov. is proposed.

Blautia-a new functional genus with potential probiotic properties?

Blautia is a genus of anaerobic bacteria with probiotic characteristics that occur widely in the feces and intestines of mammals. Based on phenotypic and phylogenetic analyses, some species in the genera Clostridium and Ruminococcus have been reclassified as Blautia, so to date, there are 20 new species with valid published names in this genus. An extensive body of research has recently focused on the probiotic effects of this genus, such as biological transformation and its ability to regulate host health and alleviate metabolic syndrome. This article reviews the origin and biological characteristics of Blautia and the factors that affect its abundance and discusses its role in host health, thus laying a theoretical foundation for the development of new functional microorganisms with probiotic properties.

Blautia liquoris sp. nov., isolated from the mud in a fermentation cellar used for the production of Chinese strong-flavour liquor

A novel Gram-positive, non-motile, non-flagellated, strictly anaerobic, non-spore-forming and dumbbell-shaped, coccoid- or chain-shaped bacterium, designated strain LZLJ-3^T, was isolated from a mud fermentation cellar which has been used for the production of Chinese strong-flavour liquor for over 100 years. Strain LZLJ-3^T grew at 20-40 °C (optimum, 37 °C), at pH 6.0-8.0 (optimum, pH 8.0) and with NaCl concentrations up to 1 % (w/v; optimum, 0 %). Phylogenetic trees established based on 16S rRNA gene sequences showed that strain LZLJ-3^T belonged to the genus Blautia of the family Lachnospiraceae, with the highest sequence similarity to Blautia stercoris GAM6-1^T (91.7 %) and Blautia faecicola KGMB01111^T (91.7 %). Comparative genome analysis showed that the orthologous average nucleotide identity (OrthoANI) and genome-to-genome distance (GGD) values between strain LZLJ-3^T and B. stercoris GAM6-1^T were respectively 69.1 and 22.9 %; the OrthoANI and GGD values between strain LZLJ-3^T and B. faecicola KGMB01111^T were respectively 70.86 and 36 % . The DNA G+C content of strain LZLJ-3^T genome was 42.1 mol%. The predominant celluar fatty acids (>10 %) of strain LZLJ-3^T were C_16 : 0 FAME (27.9 %), C_14 : 0 FAME (17.6 %) and C_16 : 0 DMA (13.0 %). Arabinose, glucose and maltose could be utilized by strain LZLJ-3^T as sole carbon sources for growth, with weak utilization of raffinose and l-fucose. API ZYM analysis gave positive reactions with α-galactosidase, β-galactosidase, α-glucosidase and β-glucosidase. The major end product of glucose fermentation was acetic acid. Based on the results of phenotypic, genotypic and phylogenetic analyses, strain LZLJ-3^T is considered to represent a novel species of Blautia, for which the name Blautia liquoris sp. nov. is proposed. The type strain is LZLJ-3^T (=KCTC 25163^T=CGMCC 1.5299^T=JCM 34225^T).

Blautia intestinalis sp. nov., isolated from human feces

A strictly anaerobic bacterial strain (27-44^T) was isolated from a stool specimen from an autistic child collected in PR China. The strain was Gram-stain-positive, non-motile, non-pigmented, non-spore-forming, and cells were oval to rod-shaped. Strain 27-44^T grew at 20-40 °C (optimal at 37 °C) and at pH 6.0-10 (optimal at 6.0-8.0). The major polar lipids were one phospholipid, two glycolipids, two aminophospholipids and one unidentified lipid. The major cellular fatty acids of strain 27-44^T were C_16 : 0 and C_17 : 0 2-OH. The end product of glucose fermentation was mainly butyric acid. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain 27-44^T was a member of the genus Blautia and phylogenetically closely related to Blautia obeum ATCC 29174^T (with 97.8 % seque nce similarity). The genome of strain 27-44^T was 3.5 Mbp with a DNA G+C content of 42.36 mol%. A total of 3436 genes were predicted and, of these, 3133 genes were annotated by KEGG. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons, strain 27-44^T represents a novel species within the genus Blautia, for which the name Blautia intestinalis sp. nov. is proposed. The type strain is 27-44^T= CGMCC 1.5285^T=NBRC 113774^T.

The Role of Fatty Acid Metabolites in Vaginal Health and Disease: Application to Candidiasis

Although the vast majority of women encounters at least one vaginal infection during their life, the amount of microbiome-related research performed in this area lags behind compared to alternative niches such as the intestinal tract. As a result, effective means of diagnosis and treatment, especially of recurrent infections, are limited. The role of the metabolome in vaginal health is largely elusive. It has been shown that lactate produced by the numerous lactobacilli present promotes health by limiting the chance of infection. Short chain fatty acids (SCFA) have been mainly linked to dysbiosis, although the causality of this relationship is still under debate. In this review, we aim to bring together information on the role of the vaginal metabolome and microbiome in infections caused by Candida. Vulvovaginal candidiasis affects near to 70% of all women at least once in their life with a significant proportion of women suffering from the recurrent variant. We assess the role of fatty acid metabolites, mainly SCFA and lactate, in onset of infection and virulence of the fungal pathogen. In addition, we pinpoint where lack of research limits our understanding of the molecular processes involved and restricts the possibility of developing novel treatment strategies.

Long-read metagenomics retrieves complete single-contig bacterial genomes from canine feces

Background

Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.

Results

We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific –Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345–, whereas others are more broadly distributed among animal and human microbiomes –Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity. Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs.

Conclusions

We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly’s contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07607-0.

Insights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages

Blautia, a genus established in 2008, is a relevantly abundant taxonomic group present in the microbiome of human and other mammalian gastrointestinal (GI) tracts. Several described (or proposed) Blautia species are available at this date. However, despite the increasing level of knowledge about Blautia, its diversity is still poorly understood. The increasing availability of Blautia genomic sequences in the public databases opens the possibility to study this genus from a genomic perspective. Here we report the pangenome analysis and the phylogenomic study of 225 Blautia genomes available in RefSeq. We found 33 different potential species at the genomic level, 17 of them previously undescribed; we also confirmed by genomic standards the status of 4 previously proposed new Blautia species. Comparative genomic analyses suggest that the Blautia pangenome is open, with a relatively small core genome (∼ 700-800 gene families). Utilizing a set of representative genomes, we performed a gene family gain/loss model for the genus, showing that despite terminal nodes suffered more massive gene gain events than internal nodes (i.e., predicted ancestors), some ancestors were predicted to have gained an important number of gene families, some of them associated with the possible acquisition of metabolic abilities. Gene loss events remained lower than gain events in most cases. General aspects regarding pangenome composition and gene gain/loss events are discussed, as well as the proposition of changes in the taxonomic assignment of B. coccoides TY and the proposition of a new species, "B. pseudococcoides.".

Lacticaseibacillus absianus sp. nov., isolated from the cecum of a mini-pig

A rod-shaped, facultative anaerobic, Gram-stain-positive bacteria, isolated from the cecum of a mini-pig, was designated as strain YH-lac23^T. Analysis of 16S rRNA gene sequences revealed that the strain was closely related to Lacticaseibacillus daqingensis JCM 33273^T (97.9 %), Lacticaseibacillus porcinae KCTC 21027^T (96.2 %) and Lacticaseibacillus manihotivorans KCTC 21010^T (95.7 %). Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. daqingensis. The average nucleotide identity value for YH-lac23^T and its most closely related strain (L. daqingensis) is 80.7 %. The main fatty acids are C_18 : 1ω9c and C_16 : 0. The cell wall contains the peptidoglycan of meso-diaminopimelic acid. The G+C content of the genomic DNA is 59.8 mol%. In view of the chemotaxonomic, phenotypic and phylogenetic properties, YH-lac23^T (=KCTC 25006=JCM 33998) represents a novel taxon. The name Lacticaseibacillus absianus sp. nov. is proposed.

Description of Paenibacillus dokdonensis sp. nov., a new bacterium isolated from soil

Two strains isolated from soil samples were designated as YH-JAE5^T and YH-JAE2. The isolates were facultative anaerobic, Gram-stain-variable, motile, rod-shaped bacteria. Phylogenetic analysis indicated that the isolates belonged to the genus Paenibacillus, but the 16S rRNA gene sequence similarities were <98 % when compared with other species within the genus. Analysis of rpoB gene revealed the isolates formed a sub-cluster with P. chibensis. The only menaquinone identified was MK-7. The two isolates contained meso-diaminopimelic acid within their cell wall peptidoglycan. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phospholipid, aminophospholipids, and lipids. The major fatty acids were C_15 : 0 anteiso and C_15 : 0 iso. The average nucleotide identity, average amino acid identity, and digital DNA-DNA hybridization values between isolate YH-JAE5^T and the most closely related reference strain (Paenibacillus chibensis KCTC 3758^T) were 81.7, 84.8 and 23.4 %, respectively. The G+C content of the genomic DNA was 47.4 mol%. Thus, the polyphasic data revealed that YH-JAE2 (=KCTC 43239=JCM 34435) and YH-JAE5^T (=KCTC 43059=JCM 33533) represent a new species. The name Paenibacillus dokdonensis sp. nov. is proposed.

Clostridium vitabionis sp. nov., isolated from the large intestine of a mini-pig

An obligately anaerobic, Gram-stain-negative, spore-forming, short rod-shaped bacterium, designated strain YH- T4B42^T, was isolated from the large intestine of a mini-pig. Phylogenetic analysis based on 16S rRNA gene sequences indicated that the isolate belongs to the genus Clostridium and is most closely related to Clostridium aminophilum KCTC 5424^T, Clostridium symbiosum KCTC 15329^T and Clostridium butyricum KCTC 1871^T, with 95.5, 92.4 and 83.0 % sequence similarity, respectively. The average nucleotide identity values for strain YH-T4B42^T and the closest related strains were lower than 72 %. The G+C content of the isolate was 55.8 mol%. The cell-wall peptidoglycan was A1γ type and contained meso-diaminopimelic acid. The predominant fatty acids were C_16 : 0, C_18 : 1 cis 9, C_14 : 0 and C_18 : 0. The major end products of glucose fermentation were lactate, formate and acetate, with a minor amount of butyrate. Based on its phenotypic, phylogenetic and chemotaxonomic properties, a novel species, Clostridium vitabionis sp. nov., is proposed for strain YH-T4B42^T (=KCTC 25105^T=NBRC 114767^T).

Lentilactobacillus kribbianus sp. nov., isolated from the small intestine of a mini pig

A Gram-stain-positive, facultative anaerobic, rod-shaped bacteria isolated from the small intestine of a mini pig was designated as strain YH-lac9^T. 16S rRNA gene sequence analysis revealed that the strain belongs to the genus Lentilactobacillus and is closely related to Lentilactobacillus senioris JCM 17472^T, Lentilactobacillus rapi JCM 15042^T and Lentilactobacillus diolivorans JCM 13927^T, with 97.6, 96.2 and 95.7 % sequence similarity, respectively. Analysis of housekeeping gene sequences (pheS and recA) revealed that the strain formed a sub-cluster with L. senioris, supporting the results of 16S rRNA gene sequences analysis. The average nucleotide identity value for YH-lac9^T and the most closely related strain is 74.1 %. The main fatty acids are C_18 : 1ω9c, summed feature 7, C_16 : 0 and summed feature 8. The G+C content of the genomic DNA is 37.8 mol%. In view of its chemotaxonomic, phenotypic and phylogenetic properties, YH-lac9^T (=KCTC 25005=JCM 33997) represents a novel taxon. The name Lentilactobacillus kribbianus sp. nov. is proposed.

Environmentally Relevant Concentration of Bisphenol S Shows Slight Effects on SIHUMIx

Bisphenol S (BPS) is an industrial chemical used in the process of polymerization of polycarbonate plastics and epoxy resins and thus can be found in various plastic products and thermal papers. The microbiota disrupting effect of BPS on the community structure of the microbiome has already been reported, but little is known on how BPS affects bacterial activity and function. To analyze these effects, we cultivated the simplified human intestinal microbiota (SIHUMIx) in bioreactors at a concentration of 45 µM BPS. By determining biomass, growth of SIHUMIx was followed but no differences during BPS exposure were observed. To validate if the membrane composition was affected, fatty acid methyl esters (FAMEs) profiles were compared. Changes in the individual membrane fatty acid composition could not been described; however, the saturation level of the membranes slightly increased during BPS exposure. By applying targeted metabolomics to quantify short-chain fatty acids (SCFA), it was shown that the activity of SIHUMIx was unaffected. Metaproteomics revealed temporal effect on the community structure and function, showing that BPS has minor effects on the structure or functionality of SIHUMIx.

Prokaryotic names: the bold and the beautiful

In recent years, names of ∼170 new genera and ∼1020 new species were added annually to the list of prokaryotic names with standing in the nomenclature. These names were formed in accordance with the Rules of the International Code of Nomenclature of Prokaryotes. Most of these names are not very interesting as specific epithets and word elements from existing names are repeatedly recycled. The rules of the Code provide many opportunities to create names in far more original ways. A survey of the lists of names of genera and species of prokaryotes shows that there is no lack of interesting names. The annotated selection presented here proves that at least some authors have exploited the possibilities allowed by the rules of the Code to name novel organisms in ways that are more attractive. I here call upon all colleagues who describe new taxa to devote more thought to the naming of new genera and species. It takes some effort, and it requires proper use of the lexicon of Classical Greek and Latin as well as an understanding of the Code and the guidelines of its orthography appendix. Creation of attractive names will boost the general interest in prokaryotic nomenclature.

Bacterial Characteristics in Intestinal Contents of Antibiotic-Associated Diarrhea Mice Treated with Qiweibaizhu Powder

Background

Qiweibaizhu powder (QWBZP) is a classical prescription of traditional Chinese medicine (TCM) to treat diarrhea in pediatric patients. Its use in health care practices and interventions has shown its effect on antibiotic-associated diarrhea (AAD). It is known that the occurrence of AAD is related to an imbalance of intestinal micro-ecology. Previous studies found that QWBZP could regulate the amount of some cultured microbes and the activities of lactase and sucrase in AAD mice. In order to investigate the treatment mechanism of QWBZP on AAD, we studied the effect of QWBZP on intestinal bacteria in a community of AAD mice.

Material/Methods

AAD mice were established by administrating the mixture of gentamycin sulfate and cefradine at the dose of 23.33 mL·kg⁻¹·d⁻¹ for 5 days. Then the AAD mice were gavaged with QWBZP decoction for 4 days and gradually recovered to a normal status. On the tenth day, the intestinal contents of mice were collected, and then the DNA was extracted for 16S rRNA sequencing followed by analysis.

Results

The analysis of bacterial 16S rRNA sequencing showed the Simpson index was decreased and the Shannon index was increased in AAD mice treated with QWBZP compared to the model group; there was no significant difference between the control group and the treatment group (P>0.05). Principle co-ordinates analysis (PCoA) indicated that there was a shorter distance between the control group and the treatment group than that between the control group and model group. At the phylum level, use of antibiotics decreased the relative abundance of Actinobacteria, Bacteroidetes, and Proteobacteria, but increased the abundance of Firmicutes and Verrucomicrobia, and the reverse changes occurred after treated with QWBZP. At the genus level, the abundance of Bacteroides and Ochrobacitrum increased in the model group, while an opposite result was observed in the treatment group. Moreover, the relative abundance of Osillospira decreased in the model group and increased in the treatment group. Genus Dorea, Coprococcus and Blautia in the model group were higher than those in the control group and further increased in the treatment group.

Conclusions

These results indicated that QWBZP improved the diarrhea syndrome with restoring the diversity and adjusting the structures of bacteria in mice intestine, which might reveal the therapeutic mechanism of QWBZP on treating AAD.

Blautia faecicola sp. nov., isolated from faeces from a healthy human

An obligately anaerobic, Gram-stain-positive, non-motile and coccoid- or oval-shaped bacterium, designated strain KGMB01111^T, was isolated from faeces from a healthy Korean. Comparative analysis of 16S rRNA gene sequences indicated that KGMB01111^T was closely related to Ruminococcus gauveauii CCRI-16110^T (93.9 %) and Blautia stercoris GAM6-1^T (93.7 %), followed by Clostridium nexile DSM 1787^T (93.5 %), Blautia producta ATCC 27340^T (93.4 %), Blautia hydrogenotrophica DSM 10507^T (93.1 %) and Blautia coccoides ATCC 29236^T (93.1 %) within the family Lachnospiraceae (Clostridium rRNA cluster XIVa). Phylogenetic analysis based on the 16S rRNA gene sequences indicated that KGMB01111^T formed a separate branch with species in the genus Blautia. The major cellular fatty acids (>10.0 %) were C_16 : 0 and C_18 : 1 cis 9 dimethyl acetal (DMA), and the major polar lipids were aminophospholipids and lipids. KGMB01111^T contained meso-diaminopimelic acid in cell-wall peptidoglycan. The predominant end product of fermentation produced by KGMB01111^T was acetic acid. Based on the whole-genome sequence, the DNA G+C content of the isolate was 44.7 mol%. On the basis of the phenotypic, chemotaxonomic and phylogenetic characteristics, KGMB01111^T represents a novel species within the genus Blautia for which the name Blautia faecicola sp. nov. is proposed. The type strain is KGMB01111^T (=KCTC 15706^T=DSM 107827^T).