16S rRNA Gene Sequence Analysis Research Articles

Prevalence and molecular characterization of ticks infesting dogs in Agartala, Tripura

Due to its ability to spread disease from one host to another, tick infestation is the most frequent issue pet owners’ deal with and should be taken seriously. The goal of the current study was to ascertain the prevalence of tick infestation in dogs in Agartala as well as its molecular identity and characterisation. A total of 1776 dogs of various breeds, ages, sexes, and categories were included in the study, which was conducted from March 2022 to February 2023 over the course of a calendar year. The total prevalence of ticks was reported to be 62.12%. According to study on breed, sex, age, and category, German spitz, male dogs, dogs under 1 year of age and stray dogs had the highest frequency of tick infestation. All throughout the year, tick infestations were seen, with the monsoon season seeing the highest frequency. Based on 16S rRNA gene amplification and sequence analysis, molecular identification revealed that all isolated ticks were members of the Rhipicephalus sanguineus species. Using a subset of the 16S rRNA gene, phylogenetic analysis revealed that R. sanguineus (OR244468.1) from Agartala (TrRS-PB) was part of the same clade as isolates from Kerala and Assam.

Microbial communities and functions are structured by vertical geochemical zones in a northern peatland

Northern peatlands are important carbon pools; however, differences in the structure and function of microbiomes inhabiting contrasting geochemical zones within these peatlands have rarely been emphasized. Using 16S rRNA gene sequencing, metagenomic profiling, and detailed geochemical analyses, we investigated the taxonomic composition and genetic potential across various geochemical zones of a typical northern peatland profile in the Changbai Mountains region (Northeastern China). Specifically, we focused on elucidating the turnover of organic carbon, sulfur (S), nitrogen (N), and methane (CH4). Three geochemical zones were identified and characterized according to porewater and solid-phase analyses: the redox interface (<10 cm), shallow peat (10–100 cm), and deep peat (>100 cm). The redox interface and upper shallow peat demonstrated a high availability of labile carbon, which decreased toward deeper peat. In deep peat, anaerobic respiration and methanogenesis were likely constrained by thermodynamics, rather than solely driven by available carbon, as the acetate concentrations reached 90 μmol·L−1. Both the microbial community composition and metabolic potentials were significantly different (p < 0.05) among the redox interface, shallow peat, and deep peat. The redox interface demonstrated a close interaction between N, S, and CH4 cycling, mainly driven by Thermodesulfovibrionia, Bradyrhizobium, and Syntrophorhabdia metagenome-assembled genomes (MAGs). The archaeal Bathyarchaeia were indicated to play a significant role in the organic carbon, N, and S cycling in shallow peat. Although constrained by anaerobic respiration and methanogenesis, deep peat exhibited a higher metabolic potential for organic carbon degradation, primarily mediated by Acidobacteriota. In terms of CH4 turnover, subsurface peat (10–20 cm) was a CH4 production hotspot, with a net turnover rate of ∼2.9 nmol·cm−3·d−1, while the acetoclastic, hydrogenotrophic, and methylotrophic methanogenic pathways all potentially contributed to CH4 production. The results of this study improve our understanding of biogeochemical cycles and CH4 turnover along peatland profiles.

Potentiality of Beneficial Microbe Bacillus siamensis GP-P8 for the Suppression of Anthracnose Pathogens and Pepper Plant Growth Promotion.

This study was carried out to screen the antifungal activity against Colletotrichum acutatum, Colletotrichum dematium, and Colletotrichum coccodes. Bacterial isolate GP-P8 from pepper soil was found to be effective against the tested pathogens with an average inhibition rate of 70.7% in in vitro dual culture assays. 16S rRNA gene sequencing analysis result showed that the effective bacterial isolate as Bacillus siamensis. Biochemical characterization of GP-P8 was also performed. According to the results, protease and cellulose, siderophore production, phosphate solubilization, starch hydrolysis, and indole-3-acetic acid production were shown by the GP-P8. Using specific primers, genes involved in the production of antibiotics, such as iturin, fengycin, difficidin, bacilysin, bacillibactin, surfactin, macrolactin, and bacillaene were also detected in B. siamensis GP-P8. Identification and analysis of volatile organic compounds through solid phase microextraction/gas chromatography-mass spectrometry (SPME/GC-MS) revealed that acetoin and 2,3-butanediol were produced by isolate GP-P8. In vivo tests showed that GP-P8 significantly reduced the anthracnose disease caused by C. acutatum, and enhanced the growth of pepper plant. Reverse transcription polymerase chain reaction analysis of pepper fruits revealed that GP-P8 treated pepper plants showed increased expression of immune genes such as CaPR1, CaPR4, CaNPR1, CaMAPK4, CaJA2, and CaERF53. These results strongly suggest that GP-P8 could be a promising biocontrol agent against pepper anthracnose disease and possibly a pepper plant growth-promoting agent.

Cellulolytic Characterization of the Rumen-isolated Acinetobacter pittii ROBY and Design of a Potential Controlled-Release Drug Delivery System

A novel cellulolytic bacterial strain, ROBY, was isolated from a bovine rumen sample using the enrichment culture method. This isolate was found to be Acinetobacter pittii, with >99% similarity according to 16S rRNA gene sequence analysis. The potential use of this strain in combination with doxorubicin (Dox)-integrated cellulose nanoparticles (Dox-CNPs) was evaluated as a proof-of-concept study for the further development of this approach as a novel controlled-release drug delivery strategy. The isolate can utilize CNPs as the sole carbon source for growth and degrade both Dox-CNPs and empty CNPs with high efficiency. Extracellular cellulases isolated from bacteria may also be used to trigger Dox release. The results also demonstrated that the release of Dox into the environment due to nanoparticle degradation in the samples incubated with Dox-CNPs significantly affected bacterial cell viability (∼75% decrease), proving the release of Dox due to bacterial cellulase activity and suggesting the great potential of this approach for further development.

Flavobacterium rivulicola sp. nov., Isolated from a Freshwater Stream.

A Gram-strain-negative, aerobic, yellow-colored, non-motile, and rod-shaped bacterial strain, designated IMCC34852T, was isolated from a freshwater stream in the Republic of Korea. Cellular growth occurred at 10-37°C, pH 6.0-9.0, and with 0-0.5% (w/v) NaCl. The 16S rRNA gene sequence analysis showed that strain IMCC34852T belonged to the genus Flavobacterium and that the strain was most closely related to F. cheonhonense ARSA-15T (97.6%), F. buctense T7T (96.7%), F. silvisoli RD-2-33T (96.1%), and F. paronense KNUS1T (96.1%). The whole-genome sequence of strain IMCC34852T was 3.2 Mbp in size, with a DNA G + C content 37.3%. The average nucleotide identities (ANI) and digital DNA-DNA hybridization (dDDH) values between strain IMCC34852T and its related species were all below 79.8% and 22.7%, respectively, which are significantly lower than the thresholds of 95% for ANI and 70% for DDH for species delineation. The major respiratory quinone of strain IMCC34852T was menaquinone-6 (MK-6) and the predominant cellular fatty acids were iso-C15:0 (32.6%), iso-C16:0 (11.7%), iso-C15:1 G (10.3%), and iso-C14:0 (6.7%). The major polar lipids of the strain were phosphatidylethanolamine, two unidentified aminolipids and six unidentified lipids. Based on these results, it was concluded that strain IMCC34852T represents a novel species in the genus Flavobacterium, for which the name Flavobacterium rivulicola sp. nov is proposed. The type strain of the proposed novel species is IMCC34852T (= KACC 23133T = KCTC 82066T = NBRC 114419T).

Altered biliary microbial and metabolic profile reveals the crosstalk between NAFLD and cholelithiasis

BackgroundThe relationship between non-alcoholic fatty liver disease (NAFLD) and cholelithiasis is intricate, with alterations in the microenvironment potentially mediating this interplay. Thus, this study aimed to explore the biliary microbiota and metabolites of patients with cholelithiasis and detect changes induced by comorbid NAFLD. MethodsIn this study, 16S rRNA gene sequencing and metabolome analysis were performed on biliary samples collected from 35 subjects. Then, patients were stratified into two groups: the comorbidity group (n = 18), consisting of cholelithiasis patients with NAFLD, and the non-comorbidity group (n = 17), comprising cholelithiasis patients without NAFLD. ResultsComorbid NAFLD did not significantly increase α-diversity but affected β-diversity. A statistically significant difference was observed in the abundance of biliary metabolites between the two groups. Specifically, differences in the abundance of 4 phyla, 19 genera, and 28 metabolites were significant between the two groups. Correlation analysis demonstrated positive associations among 12α-hydroxylated bile acid levels, Pyramidobacter and Fusobacterium abundance, AST levels, and the fibrosis-4 index (p < 0.05, r > 0.3), all of which were increased in patients with cholelithiasis and comorbid NAFLD. ConclusionsThe relationship between cholelithiasis and NAFLD influences the biliary microbial and metabolic profile, creating a detrimental microenvironment that promotes the disease progression.

Identification of Contact lens bacterial Isolates from Students of University of Benin, Nigeria, Using 16S rRNA Gene Sequence Analysis

Identification of Contact lens bacterial Isolates from Students of University of Benin, Nigeria, Using 16S rRNA Gene Sequence Analysis

Firmicutes and Bacteroidetes as the dominant microorganisms for ammonium nitrogen wastewater treatment with a low C/N ratio in BCOR

Improving nitrogen removal is a significant concern in the biological treatment of ammonium nitrogen (NH4+-N) wastewater with low chemical oxygen demand (COD)/NH4+-N (C/N) ratio, and microorganisms are the critical factor affecting nitrogen removal. In this study, a laboratory-scale biological contact oxidation reactor (BCOR) system was successfully started up (day 1 to day 47) and stabilized (day 48 to day 320). A 16S rRNA gene sequencing analysis showed that the phyla Firmicutes and Bacteroidetes were first observed as the dominant microorganisms in the BCOR for the ammonium nitrogen wastewater treatment with a low C/N ratio. The genera Bacteroides (phylum Bacteroidetes), Porphyromonas (phylum Bacteroidetes), Dialister (phylum Firmicutes), and Anaerococcus (phylum Firmicutes) also became the main microorganisms in this system for the first time. These microbial communities enabled the system to achieve an average ammonium nitrogen removal efficiency and total nitrogen removal efficiency of 95.8 % and 88.1 %, respectively, during the operational period. It indicated that these dominant microorganisms in the BCOR system played an essential role in improving the performance of biological nitrogen removal. This conclusion will play a critical role in promoting the microbial mechanism research and technology engineering application of the BCOR system for treating ammonium nitrogen wastewater with a low C/N ratio.

A Crosstalk Analysis of high-risk human papillomavirus, microbiota and vaginal metabolome in cervicovaginal microenvironment

The microbial community has a profound effect on the host microenvironment by altering metabolites. Persistent high-risk human papillomavirus (HRHPV) infection has been implicated as contributors to the initiation and progression of cervical cancer, but the involved mechanisms are unknown. Assessing the metabolic profile of the cervicovaginal microenvironment has the potential to reveal the functional interactions among the host, metabolites and microbes in HRHPV persistence infection and progression to cancer. The vaginal swabs of women were collected and divided into three groups according to the HPV HybridenPture DNA test (HC2). The participants, include 9 who were categorized as HPV-negative, 8 as positive for HPV16, and 9 as positive for HPV18. 16S rRNA gene sequencing and metabolomics analyses were applied to determine the influence of the vaginal microbiota and host metabolism on the link between HPV and cervicovaginal microenvironment. These findings revealed that HRHPV groups have unique metabolic fingerprints that distinguish them from heathy controls. We showed that HRHPV affects changes in microbial metabolic function, which has important implications for the host. Our study further demonstrated metabolite-driven complex host-microbe interactions and assist in understanding the alterations in the HRHPV-induced cervicovaginal microenvironment.

Preliminary assessment of astaxanthin production in a new Chlamydomonas strain

Green microalgae are increasingly valuable in industries such as food, cosmetics, animal feed, functional foods, and pharmaceuticals due to their ability to produce significant secondary metabolites like carotenoid pigments. Despite the growing demand for microalgae-derived carotenoids, the identification of robust wild-type strains with high biomass productivity under specific growth conditions remains limited. This study introduces Chlamydomonas sp. KIOST-2 (accession number: PP532860), a newly identified wild-type microalgal strain with 99.9 % genetic similarity to Chlamydomonas callosa, characterized through 18S rRNA gene sequence analysis. Notably, Chlamydomonas sp. KIOST-2 demonstrates considerable biomass productivity at 20–30 °C under alkaline (pH 8–10) and freshwater conditions, making it suitable for large-scale cultivation. Under drought stress, this strain forms orange cysts with high concentrations of astaxanthin (5.7 ± 0.6 mg/g) and notable lipid accumulation, primarily of oleic acid (C18:1 n9c), palmitic acid (C16:0), and linoleic acid (C18:2 n6c). The ability of Chlamydomonas sp. KIOST-2 to produce substantial amounts of astaxanthin under drought conditions without genetic modification highlights its potential for biorefinery applications and industrial exploitation. This discovery underscores the strain's unique combination of drought resistance and high astaxanthin productivity, positioning it as a valuable source of bioactive compounds for various industries.

Chronic Exposure to Petroleum-Derived Hydrocarbons Alters Human Skin Microbiome and Metabolome Profiles: A Pilot Study.

Petroleum-derived substances, like industrial oils and grease, are ubiquitous in our daily lives. Comprised of petroleum hydrocarbons (PH), these substances can come into contact with our skin, potentially causing molecular disruptions and contributing to the development of chronic disease. In this pilot study, we employed mass spectrometry-based untargeted metabolomics and 16S rRNA gene sequencing analyses to explore these effects. Superficial skin samples were collected from subjects with and without chronic dermal exposure to PH at two anatomical sites: the fingers (referred to as the hand) and arms (serving as an intersubject variability control). Exposed hands exhibited higher bacterial diversity (Shannon and Simpson indices) and an enrichment of oil-degrading bacteria (ODB), including Dietzia, Paracoccus, and Kocuria. Functional prediction suggested enriched pathways associated with PH degradation in exposed hands vs non-exposed hands, while no differences were observed when comparing the arms. Furthermore, carboxylic acids, glycerophospholipids, organooxygen compounds, phenol ethers, among others, were found to be more abundant in exposed hands. We observed positive correlations among multiple ODB and xenobiotics, suggesting a chemical remodeling of the skin favorable for ODB thriving. Overall, our study offers insights into the complex dysregulation of bacterial communities and the chemical milieu induced by chronic dermal exposure to PH.

Phenylobacterium montanum sp. nov., an oligotrophic, slightly acidophilic mesophile isolated from sandy soil.

A bacterial strain, designated S6T, was isolated from the sandy soil on a rocky mountain in South China. Cells of S6T were Gram-stain-negative, aerobic, non-spore-forming, non-motile and non-prosthecae-producing. 16S rRNA gene sequence analysis revealed the highest similarities to 12 uncultured bacteria, followed by Phenylobacterium sp. B6.10-61 (97.14 %). The closest related validly published strains are Caulobacter henricii ATCC 15253T (96.15 %), Phenylobacterium conjunctum FWC 21T (96.08 %) and Caulobacter mirabilis FWC 38T (96.08 %). Phylogenetic analysis based on 16S rRNA gene, genome and proteome sequences demonstrated that S6T formed a separated lineage in the genus Phenylobacterium. Strain S6T contained Q-10 (97.5 %) as the major ubiquinone and C18 : 1 ω7c and C16 : 0 as the major fatty acids. The polar lipid profile consisted of phosphatidylglycerol, an unknown phosphoglycolipid and three unknown glycolipids. The assembled genome comprises a chromosome with a length of 5.5 Mb and a plasmid of 96 014 bp. The G+C content was 67.6 mol%. The morphological, physiological, chemotaxonomic and phylogenetic analyses clearly distinguished this strain from its closest phylogenetic neighbours. Thus it is proposed that strain S6T represents a novel species in the genus Phenylobacterium, for which the name Phenylobacterium montanum sp. nov. is proposed. The type strain is S6T (=NBRC 115419T=GCMCC 1.18594T).

Effect of Dietary Supplementation with Organic Silicon on the Growth Performance, Blood Biochemistry, Digestive Enzymes, Morphohistology, Intestinal Microbiota and Stress Resistance in Juvenile Hybrid Tilapia (Oreochromis mossambicus × Oreochromis niloticus).

In recent decades, interest has been aroused worldwide in the use of silicon in nutrition; however, information on its effect on nutrition and metabolism of fish is limited. The objective of the research was to evaluate the effect of dietary supplementation with organic silicon on the growth performance, blood biochemistry, digestive enzymes, morphohistology and intestinal microbiota and stress resistance in hybrid Tilapia (Oreochromis mossambicus × Oreochromis niloticus). Methodologically, six levels of organic silicon (DOS) [control (0), 10, 20, 30, 40 and 50 mg·kg-1] were used to feed juvenile fish (initial weight 7.51 ± 0.25 g) grown for eight weeks in 18 aquariums (15 fish/aquarium). The results indicated that growth performance showed differences (p < 0.05) for specific growth rate, feed conversion and survival. Triglycerides, cholesterol and glucose, transaminases and digestive enzymes were significantly influenced by DOS levels. The histological study confirmed that the administered diets did not cause damage and induced significant morphological changes in the proximal intestine. The 16S rRNA gene sequencing analysis of the gut microbiota showed a high diversity and richness of OTU/Chao-1, with Fusobacteria, Proteobacteria, Bacteroidetes and Acidobacteria predominating in the DOS treatments compared to the control (p < 0.05). Induction of hypoxia stress after the feeding period showed a significant relative survival rate of 83.33% in fish fed 50 mg·kg-1. It is concluded that the DOS treatments performed better than the control treatment in most of the variables analysed. DOS had no negative effects on the fish. The results showed that up to 50 mg·kg-1 DOS improved digestive, metabolic and growth performance in hybrid Tilapia.

Methylobacterium amylolyticum sp. nov. and Methylobacterium ligniniphilum sp. nov., isolated from soil.

Two pink-pigmented bacteria, designated strains NEAU-140T and NEAU-KT, were isolated from field soil collected from Linyi, Shandong Province, PR China. Both isolates were aerobic, Gram-stain-negative, rod-shaped, and facultatively methylotrophic. 16S rRNA gene sequences analysis showed that these two strains belong to the genus Methylobacterium. Strain NEAU-140T exhibited high 16S rRNA gene sequence similarities to Methylobacterium radiotolerans NBRC 15690T (97.43 %) and Methylobacterium phyllostachyos NBRC 105206T (97.36 %). Strain NEAU-KT exhibited high 16S rRNA gene sequence similarities to M. phyllostachyos NBRC 105206T (99.00 %) and Methylobacterium longum DSM 23933T (98.72 %). A phylogenetic tree based on 16S rRNA gene sequences showed that strain NEAU-140T formed a clade with Methylobacterium aerolatum (95.94 %), Methylobacterium persicinum (95.66 %) and Methylobacterium komagatae (96.87 %), and strain NEAU-KT formed a cluster with M. phyllostachyos and M. longum. The predominant fatty acid in both strains was C18 : 1 ω7c. Both strains contained ubiquinone Q-10 as the only respiratory quinone. The polar lipid profiles of both strains contained diphosphatidylglycerol, phosphatidylethanolamine, and phosphatidylcholine. Whole-genome phylogeny showed that strains NEAU-140T and NEAU-KT formed a phyletic line with M. aerolatum, M. persicinum, Methylobacterium radiotolerans, Methylobacterium fujisawaense, Methylobacterium oryzae, Methylobacterium tardum, M. longum and M. phyllostachyos. The orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between strain NEAU-140T and its closely related strains were lower than 82.62 and 25.90 %, respectively. The ANI and dDDH values between strain NEAU-KT and its closely related strains were lower than 86.29 and 31.7 %, respectively. The genomic DNA G+C contents were 71.63 mol% for strain NEAU-140T and 69.08 mol% for strain NEAU-KT. On the basis of their phenotypic and phylogenetic distinctiveness and the results of dDDH and ANI hybridization, these two isolates represent two novel species within the genus Methylobacterium, for which the names Methylobacterium amylolyticum sp. nov. (type strain NEAU-140T=MCCC 1K08801T=DSM 110568T) and Methylobacterium ligniniphilum sp. nov. (type strain NEAU-KT=MCCC 1K08800T=DSM 110567T) are proposed.

Taxonomic diversity and environmental tolerance of cultivable extremophilic bacteria from a high-altitude meltwater pond on Ojos del Salado (Chile).

Earth harbors unique environments where only microorganisms adapted to extreme conditions, known as extremophiles, can survive. This study focused on a high-altitude meltwater pond, located in the Puna de Atacama, Dry Andes. The extremophilic bacteria of this habitat must adapt to a range of extremities, including cold and dry climate, high UV radiation, high daily temperature fluctuations, low-nutrient availability, and negative water balance. This study aimed to explore the taxonomic diversity of cultivable extremophilic bacteria from sediment samples of a desiccated, high-altitude, meltwater pond using media with different organic matter contents and different incubation temperatures. Based on the 16S rRNA gene sequence analysis, the isolates were identified as members of the phyla Actinobacteria, Proteobacteria, and Firmicutes. The most abundant genera were Arthrobacter and Pseudoarthrobacter. The isolates had oligocarbophilic and psychrotrophic properties, suggesting that they have adapted to the extreme environmental parameters of their natural habitats. The results indicate a positive correlation between nutrient concentration and temperature tolerance.

Successful operation of nitrifying granules at low pH in a continuous-flow reactor: Nitrification performance, granule stability, and microbial community

Acidic nitrification, as a novel process for treating wastewater without sufficient alkalinity, has received increasing attention over the years. In this study, a continuous-flow reactor with aerobic granular sludge was successful operated at low pH (<6.5) performing high-rate acidic nitrification. Volumetric ammonium oxidation rate of 0.4–1.2 kg/(m3·d) were achieved with the specific biomass activities of 5.8–13.9 mg N/(gVSS·h). Stable partial nitritation with nitrite accumulation efficiency over 85% could be maintained at pH above 6 with the aid of residual ammonium, whereas the nitrite accumulation disappeared when pH was below 6. Interestingly, the granule morphology significantly improved during the acidic operation. The increased secretion of extracellular polymeric substances (especially polysaccharides) suggested a self-protective behavior of microbes in the aerobic granules against acidic stress. 16S rRNA gene sequencing analyses indicated that Candidatus Nitrospira defluvii was always the dominant nitrite-oxidizing bacteria, while the dominant ammonia-oxidizing bacteria shifted from Nitrosomonas europaea to Nitrosomonas mobilis. This study, for the first time, demonstrated the improved stability of aerobic granules under acidic conditions, and also highlighted aerobic granules as a useful solution to achieve high-rate acidic nitrification.

Promethearchaeum syntrophicum gen. nov., sp. nov., an anaerobic, obligately syntrophic archaeon, the first isolate of the lineage 'Asgard' archaea, and proposal of the new archaeal phylum Promethearchaeota phyl. nov. and kingdom Promethearchaeati regn. nov.

An anaerobic, mesophilic, syntrophic, archaeon strain MK-D1T, was isolated as a pure co-culture with Methanogenium sp. strain MK-MG from deep-sea methane seep sediment. This organism is, to our knowledge, the first cultured representative of 'Asgard' archaea, an archaeal group closely related to eukaryotes. Here, we describe the detailed physiology and phylogeny of MK-D1T and propose Promethearchaeum syntrophicum gen. nov., sp. nov. to accommodate this strain. Cells were non-motile, small cocci, approximately 300-750 nm in diameter and produced membrane vesicles, chains of blebs and membrane-based protrusions. MK-D1T grew at 4-30 °C with optimum growth at 20 °C. The strain grew chemoorganotrophically with amino acids, peptides and yeast extract with obligate dependence on syntrophy with H2-/formate-utilizing organisms. MK-D1T showed the fastest growth and highest maximum cell yield when grown with yeast extract as the substrate: approximately 3 months to full growth, reaching up to 6.7×106 16S rRNA gene copies ml-1. MK-D1T had a circular 4.32 Mb chromosome with a DNA G+C content of 31.1 mol%. The results of phylogenetic analyses of the 16S rRNA gene and conserved marker proteins indicated that the strain is affiliated with 'Asgard' archaea and more specifically DHVC1/DSAG/MBG-B and 'Lokiarchaeota'/'Lokiarchaeia'. On the basis of the results of 16S rRNA gene sequence analysis, the most closely related isolated relatives were Infirmifilum lucidum 3507LTT (76.09 %) and Methanothermobacter tenebrarum RMAST (77.45 %) and the closest relative in enrichment culture was Candidatus 'Lokiarchaeum ossiferum' (95.39 %). The type strain of the type species is MK-D1T (JCM 39240T and JAMSTEC no. 115508). We propose the associated family, order, class, phylum, and kingdom as Promethearchaeaceae fam. nov., Promethearchaeales ord. nov., Promethearchaeia class. nov., Promethearchaeota phyl. nov., and Promethearchaeati regn. nov., respectively. These are in accordance with ICNP Rules 8 and 22 for nomenclature, Rule 30(3)(b) for validation and maintenance of the type strain, and Rule 31a for description as a member of an unambiguous syntrophic association.

Hypericum perforatum L. attenuates depression by regulating Akkermansia muciniphila, tryptophan metabolism and NFκB-NLRP2-Caspase1-IL1β pathway

BackgroundGut microbiota dysbiosis significantly contributes to progression of depression. Hypericum perforatum L. (HPL) is traditionally used in Europe for treating depression. However, its mechanism remains largely underexplored. PurposeThis study aims to investigate the pivotal gut microbiota species and microbial signaling metabolites associated with the antidepressant effects of HPL. MethodsFecal microbiota transplantation was used to assess whether HPL mitigates depression through alterations in gut microbiota. Microbiota and metabolic profiling of control, chronic restraint stress (CRS)-induced depression, and HPL-treated CRS mice were examined using 16S rRNA gene sequencing and metabolomics analysis. The influence of gut microbiota on HPL's antidepressant effects was assessed by metabolite and bacterial intervention experiments. ResultsHPL significantly alleviated depression symptoms in a manner dependent on gut microbiota and restored gut microbial composition by enriching Akkermansia muciniphila (AKK). Metabolomic analysis indicated that HPL regulated tryptophan metabolism, reducing kynurenine (KYN) levels derived from microbiota and increasing 5-hydroxytryptophan (5-HTP) levels. Notably, supplementation with KYN activated the NFκB-NLRP2-Caspase1-IL1β pathway and increased proinflammatory IL1β in the hippocampus of mice with depression. Interestingly, mono-colonization with AKK notably increased 5-hydroxytryptamine (5-HT) and decreased KYN levels, ameliorating depression symptoms through modulation of the NFκB-NLRP2-Caspase1-IL1β pathway. ConclusionsThe promising therapeutic role of HPL in treating depression is primarily attributed to its regulation of the NFκB-NLRP2-Caspase1-IL1β pathway, specifically by targeting AKK and tryptophan metabolites.

Lacticaseibacillus parahuelsenbergensis sp. nov., Lacticaseibacillus styriensis sp. nov. and Lacticaseibacillus zeae subsp. silagei subsp. nov., isolated from different grass and corn silage

Four rod-shaped, non-motile, non-spore-forming, facultative anaerobic, Gram-stain-positive lactic acid bacteria, designated as EB0058T, SCR0080, LD0937T and SCR0063T, were isolated from different corn and grass silage samples. The isolated strains were characterized using a polyphasic approach and EB0058T and SCR0080 were identified as Lacticaseibacillus zeae by 16S rRNA gene sequence analysis. Based on whole-genome sequence-based characterization, EB0058T and SCR0080 were separated into a distinct clade from Lacticaseibacillus zeae DSM 20178T, together with CECT9104 and UD2202, whose genomic sequences are available from NCBI GenBank. The average nucleotide identity (ANI) values within the new subgroup are 99.9 % and the digital DNA–DNA hybridization (dDDH) values are 99.3–99.9 %, respectively. In contrast, comparison of the new subgroup with publicly available genomic sequences of L. zeae strains, including the type strain DSM 20178T, revealed dDDH values of 70.2–72.5 % and ANI values of 96.2–96.6 %. Based on their chemotaxonomic, phenotypic and phylogenetic characteristics, EB0058T and SCR0080 represent a new subspecies of L. zeae. The name Lacticaseibacillus zeae subsp. silagei subsp. nov. is proposed with the type strain EB0058T (=DSM 116376T=NCIMB 15474T). According to the results of 16S rRNA gene sequencing, LD0937T and SCR0063T are members of the Lacticaseibacillus group. The dDDH value between the isolates LD0937T and SCR0063T was 67.6 %, which is below the species threshold of 70 %, clearly showing that these two isolates belong to different species. For both strains, whole genome-sequencing revealed that the closest relatives within the Lacticaseibacillus group were Lacticaseibacillus huelsenbergensis DSM 115425 (dDDH 66.5 and 65.9 %) and Lacticaseibacillus casei DSM 20011T (dDDH 64.1 and 64.9 %). Based on the genomic, chemotaxonomic and morphological data obtained in this study, two novel species, Lacticaseibacillus parahuelsenbergensis sp. nov. and Lacticaseibacillus styriensis sp. nov. are proposed and the type strains are LD0937T (=DSM 116105T=NCIMB 15471T) and SCR0063T (=DSM 116297T=NCIMB 15473T), respectively.

Isolation of Bacillus licheniformis and its protective effect on liver oxidative stress and apoptosis induced by aflatoxin B1

Aflatoxin B1 (AFB1) is one of the most toxic mycotoxins. The use of probiotics is an effective approach to reduce aflatoxins content in foods. To find efficient bacterial species that can eliminate or detoxify AFB1, a bacterial strain S51 capable of degrading AFB1 was isolated from chicken intestine and soil samples by using a culture medium containing coumarin as the sole carbon source. Based on the results of 16S rRNA gene sequence analysis, this isolate (strain S51) was identified as Bacillus licheniformis strain QT338. Further characterization of strain S51 showed that it could degrade AFB1 by 61.3% after incubation at 30°C for 72 h. Additional studies demonstrated that S51 promoted good growth performance of the treated chickens, showed no hemolytic activity, carried few drug resistance genes, and exhibited a certain level of tolerance to acid and bile salts. Furthermore, to verify whether strain S51 exerts a protective effect on AFB1-induced liver injury in chickens and to elucidate the underlying mechanism, a chicken toxicity model was induced with AFB1 (100 μg/kg BW) and treated with S51(1×109CFU/mL) for 12 d. The results showed that S51 decreased the level of alanine transaminase, aspartate transaminase, and total bilirubin (P < 0.05); increased glutathione activity and total antioxidant capacityin the liver induced by AFB1, and decreased malondialdehyde production (P < 0.05). S51 also up-regulated the mRNA expression level of the antioxidant proteins HO-1 and Nrf2 and down-regulated the expression of the oxidation-related factor Keap1 in the Nrf2/Keap1 signaling pathway (P <0.05). S51 inhibited hepatocyte apoptosis induced by AFB1 and decreased the mRNA expression levels of the apoptosis-related genes Bax, caspase-3, caspase-9, and Cyt-C (P < 0.05). These results indicate that S51 regulates apoptosis and alleviates AFB1-induced oxidative stress in chicken liver by controlling the Nrf2/Keap1 signaling pathway.