Genetic manipulation of gut microbes enables single-gene interrogation in a complex microbiome.

Hundreds of microbiota genes are associated with host biology/disease. Unraveling the causal contribution of a microbiota gene to host biology remains difficult because many are encoded by nonmodel gut commensals and not genetically targetable. A general approach to identify their gene transfer methodology and build their gene manipulation tools would enable mechanistic dissections of their impact on host physiology. We developed a pipeline that identifies the gene transfer methods for multiple nonmodel microbes spanning five phyla, and we demonstrated the utility of their genetic tools by modulating microbiome-derived short-chain fatty acids and bile acids in vitro and in the host. In a proof-of-principle study, by deleting a commensal gene for bile acid synthesis in a complex microbiome, we discovered an intriguing role of this gene in regulating colon inflammation. This technology will enable genetically engineering the nonmodel gut microbiome and facilitate mechanistic dissection of microbiota-host interactions.

Comparing the gut microbiota of Sichuan golden monkeys across multiple captive and wild settings: roles of anthropogenic activities and host factors.

BACKGROUND: Captivity and artificial food provision are common conservation strategies for the endangered golden snub-nosed monkey (Rhinopithecus roxellana). Anthropogenic activities have been reported to impact the fitness of R. roxellana by altering their gut microbiota, a crucial indicator of animal health. Nevertheless, the degree of divergence in gut microbiota between different anthropogenically-disturbed (AD) R. roxellana and their counterparts in the wild has yet to be elucidated. Here, we conducted a comparative analysis of the gut microbiota across nine populations of R. roxellana spanning China, which included seven captive populations, one wild population, and another wild population subject to artificial food provision. RESULTS: Both captivity and food provision significantly altered the gut microbiota. AD populations exhibited common variations, such as increased Bacteroidetes and decreased Firmicutes (e.g., Ruminococcus), Actinobacteria (e.g., Parvibacter), Verrucomicrobia (e.g., Akkermansia), and Tenericutes. Additionally, a reduced Firmicutes/Bacteroidetes ratiosuggested diminished capacity for complex carbohydrate degradation in captive individuals. The results of microbial functional prediction suggested that AD populations displayed heightened microbial genes linked to vitamin and amino acid metabolism, alongside decreased genes associated antibiotics biosynthesis (e.g., penicillin, cephalosporin, macrolides, and clavulanic acid) and secondary metabolite degradation (e.g., naphthalene and atrazine). These microbial alterations implied potential disparities in the health status between AD and wild individuals. AD populations exhibited varying degrees of microbial changes compared to the wild group, implying that the extent of these variations might serve as a metric for assessing the health status of AD populations. Furthermore, utilizing the individual information of captive individuals, we identified associations between variations in the gut microbiota of R. roxellana and host age, as well as pedigree. Older individuals exhibited higher microbial diversity, while a closer genetic relatedness reflected a more similar gut microbiota. CONCLUSIONS: Our aim was to assess how anthropogenic activities and host factors influence the gut microbiota of R. roxellana. Anthropogenic activities led to consistent changes in gut microbial diversity and function, while host age and genetic relatedness contributed to interindividual variations in the gut microbiota. These findings may contribute to the establishment of health assessment standards and the optimization of breeding conditions for captive R. roxellana populations.

Analysis of gut microbiota of ladybug beetle (Harmonia axyridis) after feeding on different artificial diets.

BACKGROUND: Harmonia axyridis is an effective natural enemy insect to a variety of phloem-sucking pests and Lepidopteran larvae, such as aphids, scabies, and phylloxera, while its industrial production is limited due to unmature artificial diet. Insect intestinal microbiota affect host development and reproduction. The aim of this study is to understand intestinal microbiota composition of H. axyridis and screen effective probiotics on artificial diet. Considering the role of the components and composition of the diet on the structure and composition of the intestinal microbiome, four kinds of diets were set up: (1) aphid; (2) basic diet; (3) basic diet + glucose; (4) basic diet + trehalose. The gut microbiota of H. axyridis was detected after feeding on different diets. RESULTS: Results showed that the gut microbiota between artificial diet group and aphid groups were far apart, while the basic and glucose groups were clearly clustered. Besides, the glucose group and trehalose group had one unique phylum, Cryptophyta and Candidatus Saccharibacteria, respectively. The highest abundance of Proteobacteria was found in the aphid diet. The highest abundance of Firmicutes was found in the basic diet. However, the addition of glucose or trehalose alleviated the change. In addition, the relative abundance of Enterobacter, Klebsiella, Enterobacteriaceae_unclassified, Enterobacteriales_unclassified and Serratia in the aphid group was higher than other groups. Moreover, the function of gut genes in each group also showed clear differences. CONCLUSION: These results have offered a strong link between artificial diets and gut microbes, and also have provided a theoretical basis for the screening of synergistic probiotics in artificial diet.

Correlation of gut microbial diversity to sight-threatening diabetic retinopathy.

PURPOSE: To determine the association of gut microbiome diversity and sight-threatening diabetic retinopathy (STDR) amongst patients with pre-existing diabetes. METHODS: A cross-sectional study was performed, wherein 54 participants selected in total were placed into cases cohort if diagnosed with STDR and those without STDR but had a diagnosis of diabetes mellitus of at least 10-year duration were taken as controls. Statistical analysis comparing the gut microbial alpha diversity between cases and control groups as well as patients differentiated based on previously hypothesized Bacteroidetes/Firmicutes(B/F) ratio with an optimal cut-off 1.05 to identify patients with STDR were performed. RESULTS: Comparing gut microbial alpha diversity did not show any difference between cases and control groups. However, statistically significant difference was noted amongst patients with B/F ratio ≥1.05 when compared to B/F ratio < 1.05; ACE index [Cut-off < 1.05:773.83 ± 362.73; Cut-off > 1.05:728.03 ± 227.37; p-0.016]; Chao1index [Cut-off < 1.05:773.63 ± 361.88; Cut-off > 1.05:728.13 ± 227.58; p-0.016]; Simpson index [Cut-off < 1.05:0.998 ± 0.001; Cut-off > 1.05:0.997 ± 0.001; p-0.006]; Shannon index [Cut-off < 1.05:6.37 ± 0.49; Cut-off > 1.05:6.10 ± 0.43; p-0.003]. Sub-group analysis showed that cases with B/F ratio ≥ 1.05, divided into proliferative diabetic retinopathy (PDR) and clinically significant macular edema (CSME), showed decreased diversity compared to controls (B/F ratio < 1.05). For PDR, all four diversity indices significantly decreased (p < 0.05). However, for CSME, only Shannon and Simpson indices showed significant decrease in diversity (p < 0.05). CONCLUSIONS: Based on clinical diagnosis, decreasing gut microbial diversity was observed among patients with STDR, although not statistically significant. When utilizing B/F ratio, the decreasing gut microbial diversity in STDR patients seems to be associated due to species richness and evenness in PDR when compared to decreasing species richness in CSME.

Emergence of rare and low abundant anaerobic gut Firmicutes is associated with a significant downfall of Klebsiella in human colon cancer.

Gut bacterial dysbiosis has been linked to several gastrointestinal diseases, including deadly colorectal cancer (CRC), a leading cause of mortality in cancer patients. However, perturbation in gut bacteriome during colon cancer (CC, devoid of colorectal malignancy) remains poorly explored. Here, 16S rRNA gene amplicon sequencing was carried out for fecal DNA samples targeted to hypervariable V3-V4 region by employing MiSeq platform to explore the gut bacterial community shift in CC patients. While alpha diversity indices predicted high species richness and diversity, beta diversity showed marked gut bacterial compositional dissimilarity in CC versus healthy controls (HC, n = 10 each). We observed a significant (p < 0.05, Wilcoxon Rank-Sum test) emergence of low-abundant anaerobic taxa, including Parvimonas and Peptostreptococcus, in addition to Subdoligranulum, Coprococcus, Holdemanella, Solobacterium, Bilophila, Blautia, Dorea, Moryella and several unidentified taxa, mainly affiliated to Firmicutes, in CC patients. In addition, we also traced the emergence of putative probiotic taxon Slackia, belonging to Actinomycetota, in CC patients. The emergence of anaerobic Firmicutes in CC is accompanied by a significant (p < 0.05) decline in the Klebsiella, as determined through linear discriminant analysis effect size (LEfSe) and heat tree analyses. Shifts in core microbiome and variation in network correlation were also witnessed. Taken together, this study highlighted a significant and consistent emergence of rare anaerobic Firmicutes suggesting possible anaerobiosis driving gut microbial community shift, which could be exploited in designing diagnostic and therapeutic tools targeted to CC.

Gut Microbiome and Atherosclerosis: A Mendelian Randomization Study.

Background: According to recent studies, atherosclerosis and gut microbiota are related. Nevertheless, it has been discovered that the gut microbiota varies across studies, with its function still being debated, and such relationships not proven to be causal. Thus, our study aimed to identify the key gut microbiota taxa (GM taxa) at different taxonomic levels, namely, the phylum, class, order, family, and genus, to investigate any potential causal links to atherosclerosis. Methods: We employed summary data from the MiBioGen consortium on the gut microbiota to conduct a sophisticated two-sample Mendelian randomization (MR) analysis. Pertinent information regarding atherosclerosis statistics was acquired from the FinnGen Consortium R8 publication. To assess causality, the utilized principal analytical technique was the inverse variance-weighted (IVW) method. Supplementary to IVW, additional MR methodologies were employed, including weighted median, MR-Egger, weighted methods, and simple mode. Sensitivity analyses involved the application of Cochrane's Q-test, MR-Egger intercept test, MR-PRESSO global test, and leave-one-out analysis. Results: Finally, after performing an MR study on the risk of 211 GM taxa on atherosclerosis, we discovered 20 nominal links and one strong causal link. Firmicutes (phylum ID: 1672) (odds ratio (OR) = 0.852 (0.763, 0.950), p = 0.004) continued to be connected with a lower incidence of coronary atherosclerosis, even after Bonferroni correction. Conclusions: Based on the discovered data, it was established that the phylum Firmicutes exhibits a causal relationship with a reduced occurrence of coronary atherosclerosis. This investigation could potentially provide novel insights into therapeutic objectives for atherosclerosis by focusing on the gut microbiota.

Unveiling the Gut Microbiota of Pig-Tailed Macaque (Macaca nemestrina) in Selected Habitats in Malaysia.

BACKGROUND: The gut microbiota plays an important role in primates, which may be associated with their habitat. In Malaysia, pig-tailed macaques (Macaca nemestrina) live in different habitat environments and have traditionally been used for coconut plucking for more than a century. There is currently no information regarding the gut microbiota of this macaque in Malaysia. To address this oversight, this study employed a fecal metabarcoding approach to determine the gut microbiota composition of pig-tailed macaques and establish how these microbial communities correspond with the macaque external environments of residential area, forest edge, and fragmented forest. METHODS: To determine this connection, 300 paired-end sequences of 16S rRNA were amplified and sequenced using the MiSeq platform. RESULTS: In the pig-tailed macaque fecal samples, we identified 17 phyla, 40 orders, 52 families, 101 genera, and 139 species of bacteria. The most prevalent bacterial families in the gut of pig-tailed macaques were Firmicutes (6.31%) and Proteobacteria (0.69%). Our analysis did not identify a significant difference between the type of environmental habitat and the gut microbiota composition of these macaques. CONCLUSIONS: There was great variation in the population richness and bacterial community structure. The abundance of Firmicutes and Proteobacteria helps this macaque digest food more easily while maintaining a healthy gut microbiota diversity. Exploring the gut microbiota provides an initial effort to support pig-tailed macaque conservation in the future.

Metabolic Dysfunction-Associated Fatty Liver Disease on Distinct Microbial Communities at the Bacterial Phylum Level.

INTRODUCTION: Limited data are available on the correlation between microbial communities and metabolic dysfunction-associated fatty liver disease (MAFLD). This study aimed to evaluate the influence of MAFLD on diverse microbial communities. METHODS: We recruited 43 patients with a nonviral liver disease. Enrolled patients were divided into two groups according to MAFLD criteria. The fecal microbial composition was evaluated using the variable V3-V4 region of the 16S ribosomal RNA region, which was amplified using polymerase chain reaction. First, we assessed the influence of MAFLD on distinct microbial communities at the bacterial phylum level. Next, the correlation between the microbial communities and diversity in patients with MAFLD was evaluated. RESULTS: Among the enrolled participants, the non-MAFLD and MAFLD groups consisted of 21 and 22 patients, respectively. Sequences were distributed among ten bacterial phyla. The relative abundance of Firmicutes was significantly higher in the MAFLD group than in the non-MAFLD group (p = 0.014). The microbial diversity was not significantly influenced by the presence of MAFLD (Chao-1 index: p = 0.215 and Shannon index: p = 0.174, respectively); nonetheless, the correlation coefficient between the abundances of Firmicutes and microbial diversity was higher in the non-MAFLD group than in the MAFLD group. CONCLUSION: The presence of MAFLD increased the relative abundances of Firmicutes at the bacterial phylum level, which may cause the discrepancy between the abundances of Firmicutes and diversity in patients with MAFLD.

Bacterial heat shock protein genes during induction chemotherapy in pediatric patients with acute lymphoblastic leukemia.

Background: Heat shock proteins (HSP) protect cancer cells. Gastrointestinal bacteria contain HSP genes and can release extracellular vesicles which act as biological shuttles. Stress from treatment may result in a microbial community with more HSP genes, which could contribute to circulating HSP levels. Methods: The authors examined the abundance of five bacterial HSP genes pre-treatment and during induction in stool sequences from 30 pediatric acute lymphoblastic leukemia patients. Results: Decreased mean HTPG counts (p = 0.0024) pre-treatment versus induction were observed. During induction, HTPG, Shannon diversity and Bacteroidetes decreased (p = 7.5e-4; 1.1e-3; 8.6e-4), while DNAK and Firmicutes increased (p = 6.9e-3; 9.2e-4). Conclusion: Understanding microbial HSP gene community changes with treatment is the first step in determining if bacterial HSPs are important to the tumor microenvironment and leukemia treatment.

Preparation of Mn modified waste dander biochar and its effect on soil carbon sequestration.

In order to reduce the mineralization of soil organic carbon (SOC) and enhance the ability of soil carbon sequestration. Mn-modified waste dander biochar (Mn-BC) was successfully prepared via impregnation and pyrolysis, and MnSO4 was formed on its surface. Mn-BC increases the carbon retention and reduces the emissions of CO2 and SO2 in way of forming CO, Mn-O-C bond and MnSO4. At the same time, the stability of the original biochar was reserved due to forming a conjugated structure (CC and pyridine-N bond), and the carbon sequestration content was increased to 25.63%. Importantly, the application of Mn-BC can directly regulate the transformation of microbial bacterial community and lead to create stable carbon dominant bacteria (Firmicutes). And the mineralization rate of SOC is reduced to 0.48 mg CO2/(g·d), together with an increased content of TOC (48.16%), thus the purpose of efficient carbon sequestration is achieved in soil.

In Silico Screening of Bacteriocin Gene Clusters within a Set of Marine Bacillota Genomes.

Due to their potential application as an alternative to antibiotics, bacteriocins, which are ribosomally synthesized antimicrobial peptides produced by bacteria, have received much attention in recent years. To identify bacteriocins within marine bacteria, most of the studies employed a culture-based method, which is more time-consuming than the in silico approach. For that, the aim of this study was to identify potential bacteriocin gene clusters and their potential producers in 51 marine Bacillota (formerly Firmicutes) genomes, using BAGEL4, a bacteriocin genome mining tool. As a result, we found out that a majority of selected Bacillota (60.78%) are potential bacteriocin producers, and we identified 77 bacteriocin gene clusters, most of which belong to class I bacteriocins known as RiPPs (ribosomally synthesized and post-translationally modified peptides). The identified putative bacteriocin gene clusters are an attractive target for further in vitro research, such as the production of bacteriocins using a heterologous expression system.

High poly-γ-glutamic acid-containing natto improves lipid metabolism and alters intestinal microbiota in mice fed a high-fat diet.

Several beneficial effects of poly-γ-glutamic acid (γ-PGA) have been reported. To test whether natto, a fermented soy food rich in γ-PGA, can improve intestinal microbiota content and lipid metabolism in a high-fat diet, we compared the intestinal microbiota content, plasma, liver, and fecal contents, and changes in gene expression in the livers and large intestines of a group of mice fed a high-fat diet supplemented with cooked soybeans (SC group) and a group fed a high-fat diet supplemented with natto (NA group) for 42 days; high-fat diet-fed mice were used as a control (Con group). Hepatic lipid levels were significantly lower, the fecal bile acid and lipid levels were significantly greater, and the Bacteroidetes/Firmicutes ratio was significantly higher in the SC and NA groups as compared to Con group. Additionally, plasma glucose and triglyceride levels, the expression of liver fatty acid synthase, and the relative abundance of Lactobacillaceae was significantly higher in the NA group than in the Con group. Although both natto and cooked soybeans impacted the metabolic response to a high-fat diet, the addition of natto had a greater effect on glucose and lipid metabolism. γ-PGA may play an important role in natto functionality.

Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment.

BACKGROUND: The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies. RESULTS: The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals. CONCLUSION: Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.

Host-Microbiota Interactions in the Esophagus During Homeostasis and Allergic Inflammation.

BACKGROUND & AIMS: Microbiota composition and mechanisms of host-microbiota interactions in the esophagus are unclear. We aimed to uncover fundamental information about the esophageal microbiome and its potential significance to eosinophilic esophagitis (EoE). METHODS: Microbiota composition, transplantation potential, and antibiotic responsiveness in the esophagus were established via 16S ribosomal RNA sequencing. Functional outcomes of microbiota colonization were assessed by RNA sequencing analysis of mouse esophageal epithelium and compared with the human EoE transcriptome. The impact of dysbiosis was assessed using a preclinical model of EoE. RESULTS: We found that the murine esophagus is colonized with diverse microbial communities within the first month of life. The esophageal microbiota is distinct, dominated by Lactobacillales, and demonstrates spatial heterogeneity as the proximal and distal esophagus are enriched in Bifidobacteriales and Lactobacillales, respectively. Fecal matter transplantation restores the esophageal microbiota, demonstrating that the local environment drives diversity. Microbiota colonization modifies esophageal tissue morphology and gene expression that is enriched in pathways associated with epithelial barrier function and overlapping with genes involved in EoE, including POSTN, KLK5, and HIF1A. Finally, neonatal antibiotic treatment reduces the abundance of Lactobacillales and exaggerates type 2 inflammation in the esophagus. Clinical data substantiated loss of esophageal Lactobacillales in EoE compared with controls. CONCLUSIONS: The esophagus has a unique microbiome with notable differences between its proximal and distal regions. Fecal matter transplantation restores the esophageal microbiome. Antibiotic-induced dysbiosis exacerbates disease in a murine model of EoE. Collectively, these data establish the composition, transplantation potential, antibiotic responsiveness, and host-microbiota interaction in the esophagus and have implications for gastrointestinal health and disease.

Investigation of milk microbiota of healthy and mastitic Sahiwal cattle.

BACKGROUND: Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis. RESULTS: Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups. CONCLUSION: It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.

Enhancing defense against rice blast disease: Unveiling the role of leaf endophytic firmicutes in antifungal antibiosis and induced systemic resistance.

Rice remains the primary staple for more than half of the world's population, yet its cultivation faces numerous challenges, including both biotic and abiotic stresses. One significant obstacle is the prevalence of rice blast disease, which substantially diminishes productivity and increases cultivation costs due to frequent fungicide applications. Consequently, the presence of fungicide residues in rice raises concerns about compliance with international maximum residue limits (MRLs). While host resistance has proven effective, it often remains vulnerable to new variants of the Magnaporthe oryzae pathogen. Therefore, there is a critical need to explore innovative management strategies that can complement or enhance existing methods. An unexplored avenue involves harnessing endophytic bacterial communities. To this end, the present study investigates the potential of eleven endophytic Bacillus spp. in suppressing Pyricularia oryzae, promoting plant growth, and eliciting a defense response through phyllobacterization. The results indicate that the secreted metabolome and volatilome of seven tested isolates demonstrate inhibitory effects against P.oryzae, ranging from a minimum of 40% to a maximum of 70%. Bacillus siamensis L34, B. amyloliquefaciens RA37, B. velezensis L12, and B. subtilis B18 produce antifungal antibiotics targeting P.oryzae. Additionally, B. subtilis S4 and B. subtilis S6 emerge as excellent inducers of systemic resistance against blast disease, as evidenced by elevated activity of biochemical defense enzymes such as peroxidase, polyphenol oxidase, and total phenol content. However, a balance between primary metabolic activity (e.g., chlorophyll content, chlorophyll fluorescence, and photosynthetic rate) and defense activity is observed. Furthermore, specific endophytic Bacillus spp. significantly stimulates defense-related genes, including OsPAD4, OsFMO1, and OsEDS1. These findings underscore the multifaceted potential of endophytic Bacillus in managing blast disease through antibiosis and induced systemic resistance. In conclusion, this study highlights the promising role of endophytic Bacillus spp. as a viable option for blast disease management. Their ability to inhibit the pathogen and induce systemic resistance makes them a valuable addition to the existing strategies. However, it is crucial to consider the trade-off between primary metabolic activity and defense response when implementing these bacteria-based approaches.

Assessment of Lactobacillus rhamnosus mediated protection against arsenic-induced toxicity in zebrafish: a qPCR-based analysis of Firmicutes and Bacteroidetes groups and embryonic development.

Arsenic poses a significant health risk worldwide, impacting the gut microbiota, reproductive health, and development. To address this issue, a cost-effective method like probiotic supplementation could be beneficial. However, the interplay between arsenic toxicity, probiotics, gut microbiota, and maternal transcript modulation remains unexplored. This study investigates the impact of Lactobacillus rhamnosus (L. rhamnosus) DSM 20021 on the proportions of Firmicutes and Bacteroidetes, as well as its effects on embryonic development in zebrafish induced by arsenic trioxide (As2O3). Adult zebrafish were exposed to both high and environmentally relevant concentrations of As2O3 (10, 50, and 500 ppb) for 1, 6, and 12 weeks. qPCR analysis revealed increased proportions of Firmicutes and Bacteroidetes in all As2O3-exposed and As2O3 + L. rhamnosus-exposed groups, while no significant changes were observed in groups exposed only to L. rhamnosus DSM 20021. The larvae, exposed to 500 ppb of As2O3 for 12 weeks, exhibited low growth, decreased survival rates, and morphological deformities. However, these adverse effects were reversed upon exposure to only L. rhamnosus DSM 20021. Furthermore, the expression of DVR1 and ABCC5, which are involved in defense against xenobiotics and embryo development, decreased significantly in As2O3 (500 ppb) and As2O3 (500 ppb) + L. rhamnosus-exposed groups, whereas ameliorative effects were observed in only L. rhamnosus DSM 20021-exposed groups.

Request for an Opinion on the standing and retention of Firmicutes as a phylum name.

Oren and Garrity recently published 42 new prokaryotic phylum names, including Bacillota, which they describe as a synonym of the effectively published name Firmacutes and its orthographic correction Firmicutes. However, the name Firmacutes was listed as a division in the Approved Lists of Bacterial Names, which suggests that it should be treated as having been validly published. Recent emendations to rules require that a named phylum now requires a named type genus and a phylum name is formed by the addition of the suffix -ota to the stem of the name of the designated type genus. However, there are strong practical arguments for retaining the name Firmicutes, notwithstanding the uncertainty over whether the name already has standing. This matter is referred to the Judicial Commission, asking for an opinion on the standing and retention of the name Firmicutes.

Paenibacillus sedimenti sp. nov., isolated from freshwater wetland sediment.

A Gram-stain-positive, motile, rod-shaped, facultatively anaerobic bacterium, designated strain WST5T, isolated from sediment was characterized using a polyphasic approach. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain WST5T was most closely related to Paenibacillus aestuarii CJ25T (96.8 % similarity). The genome size of the WST5T was 6.5 Mb, contained 4500 predicted protein-coding genes, and had a DNA G+C content of 46.6%. The values of whole-genome average nucleotide identity analysis and digital DNA-DNA hybridization between strain WST5T and its closely related type strains were less than 76 and 25.6 %, respectively. The predominant cellular fatty acids (>10 %) were anteiso-C15 : 0 and C16 : 1 ω5c and the main menaquinone was MK-7. The major polar lipids were identified as diphospholidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and two unknown aminophospholipids. Based on the results of phenotypic, genotypic, chemotaxonomic and phylogenetic analyses, strain WST5T is considered to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus sedimentum sp. nov. is proposed. The type strain is WST5T (=NBRC 115194 T=CGMCC 1.18706T).

Chakrabartyella piscis gen. nov., sp. nov., a member of the family Lachnospiraceae, isolated from the hindgut of the marine herbivorous fish Kyphosus sydneyanus.

A Gram-stain-negative, non-spore-forming, rod-shaped, obligately anaerobic bacterium, designated strain BP5GT, was isolated from the hindgut of a silver drummer (Kyphosus sydneyanus) fish collected from the Hauraki Gulf, New Zealand. Phylogenetic analysis based on the 16S rRNA gene sequence indicated that the isolate belonged to the family Lachnospiraceae in the phylum Bacillota and was most closely related to Anaerotignum propionicum with 94.06 % sequence identity. Isolate BP5GT grew on agar medium containing mannitol and fish gut fluid as carbon sources. Clear colonies of approximately 1 mm diameter of the isolate grew within a week at 20-28 °C (optimum, 28 °C) and pH 7.6-8.5 (optimum, pH 8.5). Strain BP5GT was very sensitive to NaCl and the optimal concentration for growth was 0.045 % (w/v). Acetate and propionate were the major fermentation products. The major cellular fatty acids were C12 : 0, C14 : 0, C15 : 0 and C16 : 0. The genome sequence of the isolate was determined. Its G+C content was 38.41 mol% and the 71.41 % average nucleotide identity of the BP5GT genome to its closest neighbour with a sequenced genome (A. propionicum DSM 1682T) indicated low genomic relatedness. Based on the phenotypic and taxonomic characteristics observed in this study, a novel genus and species named Chakrabartyella piscis gen. nov., sp. nov. is proposed for isolate BP5GT (=ICMP 24687T=JCM 35769T).