Abundant Genera Research Articles

Mendelian randomization identifies causal associations between GWAS-associated bacteria and their metabolites and rheumatoid arthritis.

Accumulating evidence suggests that an imbalance of gut microbiota is commonly observed in patients with rheumatoid arthritis (RA). However, it remains unclear whether gut microbiota dysbiosis is a cause or consequence of RA, and the mechanisms by which gut dysbiosis contributes to RA have not been fully understood. This study aimed to investigate the causal relationship between gut microbiota and metabolites with RA. A two-sample Mendelian randomization analysis was performed to estimate the causality of gut microbiota and metabolites on RA. A genome-wide association study (GWAS) of 211 gut microbiota and 217 metabolites was used as the exposure, whereas RA was treated as the outcome. Inverse variance weighted (IVW) was regarded as the primary approach for calculating causal estimates. MR Egger method, Weighted median method, Simple mode method, and weighted mode method were used for sensitive analysis. Metabolic pathway analysis was performed via the web-based Metaconflict 5.0. Additionally, an animal study was undertaken to evaluate the results inferred by Mendelian randomization. This study indicated that six gut microbiota taxa (RuminococcaceaeUCG013, Erysipelotrichia, Erysipelotrichaceae, Erysipelotrichales, Clostridia, and Veillonellaceae) were estimated to exert a positive impact on RA. Conversely, seven gut microbiota taxa (Oxalobacter, Cyanobacteria, RuminococcaceaeUCG002, LachnospiraceaeUCG010, Christensenellaceae, Oxalobacteraceae, Anaerostipes) were estimated to exert a negative impact on RA. Three metabolites, namely indole-3-propionate (IPA), glycine and sphingomyelin (SM 16:1), were found to be linked to lower RA risk, while five metabolites (argininosuccinate, CE 20_4, TAG 58_8, PC 40_6, and LPC 20_4) were linked to higher RA risk. Additionally, four metabolic pathways were identified by metabolic pathway analysis. The collagen-induced arthritis (CIA) rats exhibited a higher relative abundance of Class_Clostridia and a lower abundance of Genus_Lachnospiraceae (p < 0.05) than the healthy controls. This study identified causal associations between specific gut microbiota, metabolites, and RA. These findings support the significant role of gut microbiota and metabolites in RA pathogenesis.

Insight into the differential response of functional denitrifiers to novel formulated organic amendments in soybean agroecosystem

Fertilizer application has been known to cause substantial changes in the microbial composition of agricultural soil. Therefore, there is a need for more fertilizer management practices that will improve nitrogen (N) content, which is the key restrictive factor for microbial growth. To elucidate the characteristics of these fertilizers in the soil, samples were collected from a soybean field of control (S0) with no addition of organic amendment, biochar made from rice straw (S1), compost made from cattle manure and maize straw at a ratio of 5:1 (S2), composting S2 + 10 % S1 (S3), and mixture of S2 + 10 % S1 without composting (S4). The soil functional denitrifiers (nirS and nirK) were unravelled using Illumina high-throughput sequencing. It was observed that S3 (66.56 %) and S4 (61.14 %) increased the NO3−-N, while S2 increased the total Kjeldahl nitrogen (TKN) by 15.79 % compared to S0. OTU847_norank_p_environmental_samples in nirS and OTU112_unclassified_f_Bradyrhizobiaceae in nirK were the most abundant genera in S1-S4 while S2 and S3 had the highest unique OTUs in nirK and nirS communities, respectively. The canonical correspondence analysis (CCA) showed that NO2−-N and nitrate reductase (NIR) enzyme-shaped nirS and nirK denitrifiers. Also, from the structural equation model (SEM), TKN showed a higher negative significant effect on nirK alpha and beta diversities, while S4 showed the lowest positive network in nirS and nirK- denitrifiers. Meanwhile, Bradyrhizobium was observed as a common genus in the multivariate co-occurrence network in nirS- and nirK-type denitrifiers. This study provides the theoretical basis and technical support that single and combined fertilizers could influence nirS and nirK denitrifiers in soybean-grown soil.

Similar In Vitro Ileal Fermentation Outcomes Validate the Use of a Pig Ileal Inoculum in an In Vitro Fermentation Assay for the Adult Human

BackgroundAn in vivo/in vitro ileal fermentation assay using growing pigs has shown important fermentability and organic acid production. This assay could be used to study human foods but needs validation. ObjectivesA pig inoculum for studying human ileal fermentation was used to compare the in vitro fermentation of fiber substrates using ileal inocula prepared from growing pigs or human ileostomates. MethodsTen pigs (19 ± 4.5 kg bodyweight, mean ± standard deviation) received a diet containing human foods. After 2 wk, ileal digesta were collected 5 h postmeal. Five recruited human ileostomates incorporated the same human foods into their diet for a week before consuming 2 meals similar to the pigs’ diet. Ileal effluents were then collected from 2 to 6 h postmeal. The porcine ileal digesta and human ileal effluents were used for microbial analysis and in vitro fermentation of arabinogalactan, fructooligosaccharides, and pectin. ResultsThe in vitro organic matter fermentability of arabinogalactan, fructooligosaccharides, and pectin was similar (P > 0.05) between the pig and human ileal inocula (34 ± 2.13% on average). Regardless of substrates, the propionic and lactic acid production was similar between humans and pigs (P > 0.05). Ninety percent of the ileal bacterial genera were found in similar (P > 0.05) numbers in pigs and human ileostomates, which accords with the similar (P > 0.05) Shannon diversity index and predicted metabolic activity. However, some of the most abundant genera were different between species, such as Granulicatella which had 83-fold greater (P ≤ 0.05) numbers in human ileostomates, and Lactobacillus had 272-fold greater (P ≤ 0.05) numbers in pigs. ConclusionsThe in vitro ileal fermentation patterns were similar across species despite some ileal microbial compositional differences, suggesting that the growing pig could be used as a model to provide an ileal inoculum for studying ileal fermentation in adult humans.This trial was registered at the Australian New Zealand Clinical Trials registry as ACTRN12622000813785.

Optimizing the microbial community composition in anaerobic digesters to improve biogas yields from food waste

Methods: Food waste collected from local restaurants and households in New York city will be used in this study. The food waste will be characterized to analyze its composition. Batch anaerobic digesters will be inoculated with microbial communities from existing food waste digesters. DNA analysis using 16S rRNA gene sequencing will be done to show the initial microbial consortia. Various perturbations will be applied to the digesters including changes in temperature, pH, feeding rates, mixing intensities to select for microbial populations yielding higher biogas production. Biogas production will be monitored over time. DNA analysis will be repeated after perturbation to analyze changes in the microbial community structure. Results: Preliminary results show Food waste characterized was found to contain 35% proteins, 45% carbohydrates and 20% fats. The initial microbial consortia in the digesters was dominated by bacteria from the genera Clostridium, Bacteroides and Methanothermobacter. Increasing feeding rates led to a 40% increase in biogas yields. Microbial analysis indicated a shift in populations with Clostridium becoming the most abundant genus. Decreasing pH from 7 to 6.5 further enhanced biogas by 25% with Clostridium and Syntrophomonas becoming dominant. Discussion: The study demonstrates that optimizing operational conditions can effectively manipulate the microbial communities in anaerobic digesters processing food waste. By applying selective pressures, populations better suited to degrade the local food waste and produce higher methane yields can be enriched. Further experiments will aim to construct stable, optimized consortia through controlled perturbation for robust and efficient food waste digestion. The approach holds promise for improving biogas production from food waste globally

The Response of Murine Gut Microbiome in the Presence of Altered rpoS Gene of Klebsiella pneumoniae.

The murine model is invaluable for studying intricate interactions among gut microbes; hosts; and diseases. However; the impact of genetic variations in the murine microbiome; especially in disease contexts such as Klebsiella pneumoniae (Kp) infection; still needs to be explored. Kp; an opportunistic global pathogen; is becoming increasingly prevalent in regions like Asia; especially China. This study explored the role of the gut microbiota during Kp infection using mouse model; including wild-type and rpoS mutants of Kp138; KpC4; and KpE4 from human; maize; and ditch water; respectively. Under stress conditions; RpoS reconfigures global gene expression in bacteria; shifting the cells from active growth to survival mode. Our study examined notable differences in microbiome composition; finding that Lactobacillus and Klebsiella (particularly in WKp138) were the most abundant genera in mice guts at the genus level in all wild-type treated mice. In contrast; Firmicutes were predominant in the healthy control mice. Furthermore; Clostridium was the dominant genus in all mutants; mainly in ∆KpC4; and was absent in wild-type treated mice. Differential abundance analysis identified that these candidate taxa potentially influence disease progression and pathogen virulence. Functional prediction analysis showed that most bacterial groups were functionally involved in biosynthesis; precursor metabolites; degradation; energy generation; and metabolic cluster formation. These findings challenge the conventional understanding and highlight the need for nuanced interpretations in murine studies. Additionally; this study sheds light on microbiome-immune interactions in K. pneumoniae infection and proposes new potential therapeutic strategies.

Examination of sex-specific interactions between gut microbiota and host metabolism after 12-week combined polyphenol supplementation in individuals with overweight or obesity

ABSTRACT Polyphenols exert beneficial effects on host metabolism, which may be mediated by the gut microbiota. We investigated sex-specific differences in microbiota composition and interactions with cardiometabolic parameters after polyphenol supplementation in individuals with overweight/obesity. In a double-blind, randomized, placebo-controlled trial, 19 women and 18 men with normal glucose tolerance and body mass index >25 kg/m2 received epigallocatechin-3-gallate and resveratrol (EGCG+RES, 282 + 80 mg/d) or placebo supplements for 12 weeks. Fecal microbiota composition (16S rRNA gene amplicon sequencing, V3-V4 region), in vivo whole-body fat oxidation (indirect calorimetry), and mitochondrial respiration in permeabilized skeletal muscle fibers (SkM-Ox; ex vivo respirometry) were determined pre- and post-intervention. Overall, EGCG+RES supplementation did not affect gut microbiota composition. Akkermansia, Ruminococcaceae UCG-002, Subdoligranulum, and Lachnospiraceae UCG-004 were more abundant, while Veillonella, Tyzzerella 4, Clostridium innocuum group, Ruminococcus gnavus group, Escherichia-Shigella, and an uncultured Ruminococcaceae family genus were less abundant in women compared to men. In women, only baseline Eubacterium ventriosum group abundance correlated with EGCG+RES-induced changes in SkM-Ox. In men, low Dorea, Barnsiella, Anaerotruncus, Ruminococcus, Subdoligranulum, Coprococcus, Eubacterium ventriosum group, Ruminococcaceae UCG-003, and a Ruminococcaceae family genus abundance, and high Blautia abundance at baseline were associated with improvements in SkM-Ox. Changes in whole-body fat oxidation were not associated with gut microbiota features. We conclude that baseline microbiota composition predicts changes in SkM-Ox as a result of EGCG+RES supplementation in men but not in women. Men may be more prone to diet-induced, gut microbiota-related improvements in cardiometabolic health. These sex-differences should be further investigated in future precision-based intervention studies.

Gut dysbiosis of Rana zhenhaiensis tadpoles after lead (Pb) exposure based on integrated analysis of microbiota and gut transcriptome

Lead (Pb) is a ubiquitously detected heavy metal pollutant in aquatic ecosystems. Previous studies focused mainly on the response of gut microbiota to Pb stress, with less emphasis on gene expression in intestine, thereby limiting the information about impacts of Pb on intestinal homeostasis in amphibians. Here, microbial community and transcriptional response of intestines in Rana zhenhaiensis tadpoles to Pb exposure were evaluated. Our results showed that 10 μg/L Pb significantly decreased bacterial diversity compared to the controls by the Simpson index. Additionally, 1000 μg/L Pb exposure resulted in a significant reduction in the abundance of Fusobacteriota phylum and Cetobacterium genus but a significant expansion in Hafnia-Obesumbacterium genus. Moreover, transcriptome analysis revealed that about 90 % of the DEGs (8458 out of 9450 DEGs) were down-regulated in 1000 μg/L Pb group, mainly including genes annotated with biological functions in fatty acid degradation, and oxidative phosphorylation, while up-regulated DEGs involved in metabolism of xenobiotics by cytochrome P450. The expression of Gsto1, Gsta5, Gstt4, and Nadph showed strong correlation with the abundance of genera Serratia, Lactococcus, and Hafnia-Obesumbacterium. The findings of this study provide important insights into understanding the influence of Pb on intestinal homeostasis in amphibians.

Causal relationship between gut microbiota and diabetic complications: a two-sample Mendelian randomization study

BackgroundImbalances in gut microbiota (GM) have been proposed as a potential contributing factor to diabetic complications; however, the causal relationship remains incompletely understood.MethodsSummary statistics were obtained from genome-wide association studies (GWAS) of 196 gut microbial taxa, including 9 phyla, 16 classes, 20 orders, 32 families, and 119 genera. These data were then analyzed using mediation Mendelian randomization (MR) analyses to explore the potential mediating effect of diabetes complications risk factors on the relationship between gut microbiota and specific diabetic complications such as diabetic kidney disease (DKD), ketoacidosis, and diabetic retinopathy (DR).ResultsIn our Mendelian analysis, we observed negative associations between Bifidobacterial order and Actinomycete phylum with DKD in type 1 diabetes (T1D) as well as early DKD in T1D. Conversely, these taxa showed positive associations with ketoacidosis in type 2 diabetes (T2D). In reverse Mendelian analysis, we found that DR in both T1D and T2D as well as ketoacidosis in T2D affected the abundance of Eubacterium fissicaten genus and LachnospiraceaeUCG010 family within the gut microbiota.ConclusionsOur findings provide compelling evidence for causal relationships between specific GM taxa and various diabetes complications. These insights contribute valuable knowledge for developing treatments targeting diabetes-related complications.

Identification of microbial antigens in liver tissues involved in the pathogenesis of primary biliary cholangitis using 16S rRNA metagenome analysis.

Multiple factors are involved in the pathogenesis of primary biliary cholangitis (PBC), a chronic cholestatic liver disease, characterized by intrahepatic cholangiopathy. In particular, studies have suggested that environmental factors such as the presence of granulomas in the portal vein region are important for the development of PBC. This study aimed to comprehensively analyze and identify foreign-derived antigens in PBC liver tissue to confirm their involvement in PBC pathogenesis. Portal areas and hepatocyte regions were selectively dissected from formalin-fixed paraffin-embedded PBC liver tissue samples using the microlaser method, followed by total DNA extraction. We then validated whether the bacterial strains identified through 16S rRNA metagenomic analysis were detected in PBC liver tissues. The most frequently detected bacterial genera in the PBC liver tissue samples were Sphingomonas panacis, Providencia, and Cutibacterium. These bacterial genera were also detected in the other PBC samples. Validation for the detection of S. panacis, the most abundant genus, revealed polymerase chain reaction bands extracted from the portal areas of all samples. They were also more highly expressed than bands detected in the hepatocyte region. S. panacis antigen was specifically detected in the portal areas of PBC liver tissues. The introduction of foreign-derived antigens into the liver as an environmental factor could be a possible mechanism for the development of PBC.

Metaviromic reveals the dynamics and diversity of the virosphere in wastewater samples from Natal, Brazil

The COVID-19 pandemic underscored the significance of omics technology and Wastewater-Based Epidemiology for epidemic preparedness. This study investigates the virosphere in wastewater samples from Natal (Brazil), aiming to understand its structure, relationships, and potential. Metaviromic analysis was used on DNA and RNA from weekly samples collected over a year (June/2021 to May/2022) from three wastewater treatment plants. The virosphere showed stability, particularly in viruses infecting microorganisms and plants. However, an alternation of representatives of viruses that infect animals has been observed. Among the most abundant viruses infecting microorganisms are genera associated with the bacterial genera Escherichia, Pseudomonas, and Caulobacte. Regarding the viruses infecting plants, Sobemovirus and Tobamovirus are the most abundant genera. Odontoglossum ringspot virus was identified as a possible RNA virus biomarker. Among DNA viruses infecting animals, genera Bocaparvovirus and Mastadenovirus are the most prevalent. Intriguingly, some Poxviridae family members were observed in the samples. Co-occurrence network analysis identified potential biomarkers like Volepox virus, Anatid herpesvirus 1, and Caviid herpesvirus 2. Among RNA viruses affecting animals, Mamastrovirus, Rotavirus, and Norovirus genera were the most abundant pathogens. Furthermore, members of the Coronaviridae family exhibited a high degree of centrality values in the co-occurrence network, even connecting with unclassified viruses. The study emphasizes the importance of research in understanding the roles of unclassified viruses. In addition, we observed an association between Coronaviridae reads, rainfall, and the number of reported COVID-19 cases. Our study highlights the diversity and complexity of the viral community in wastewater and the need for research to understand better the ecological roles unclassified viruses play. Such advances will significantly contribute to our preparedness and response to future viral threats. Furthermore, our study contributes to knowledge of virosphere dynamics, offering insights that can contribute to the direction of future public health policies and interventions.

Energy reserves and gut microbiota of marine mussels under combined exposure to pathogens and predation risk

In recent years, environmental issues such as eutrophication have led to proliferation of pathogenic bacteria and deterioration of aquaculture environmental water quality. However, the impact of pathogenic bacteria on the mussel-predator food chain in the marine environment is not yet fully understood. In this experiment, mussels were cultured with crabs (Charybdis japonica) for 14 days. Then crabs were retained or removed and pathogenic bacteria (Vibrio alginolyticus) was added and mussels were cultured for 3 days. C. japonica and V. alginolyticus were used as two stressors to explore their effects on energy content and gut microbiota of Mytilus coruscus. The metabolic parameters (protein, carbohydrate and lipid contents) of the gills and digestive glands, and the gut microbiota of the mussels were measured. The study found that presence of predation risk significantly increased the content of protein but decreased carbohydrate and lipid contents in the gills at 14th day. After 17 days of exposure, the presence of predation risk significantly reduced protein content but significantly increased lipid content in gills of mussel. The protein content in digestive gland was significantly increased, but the lipid content was significantly decreased. The presence of predation risk and pathogens had interactive effect on the protein content in the digestive glands of mussels. The presence of V. alginolyticus and predation risk affected the community structure, species richness, and diversity of gut microbiota. The most abundant phyla noted were Bacteroidota, Proteobacteria, and Firmicutes, and the most abundant genus noted were Prevotella, Klebsiella and Dialister. Alpha diversity analysis and beta diversity analysis revealed that the presence of V. alginolyticus and predation risk altered the microbial community structure. V. alginolyticus plays a positive role in the harmful microbiota of gut microbiota. The proportion of Bacteroidota and Proteobacteria in intestinal bacteria increased significantly. Linear discriminant analysis effect size (LEfSe) showed that the biomarkers in each group are significantly different at the genus level. Significant correlations between metabolic parameters (protein content and carbohydrate content) and the level of KEGG function prediction (amino acid metabolism and carbohydrate metabolism) were observed in gills and digestive glands. This study highlights the priority of energy responses in mussels under dual predator-pathogen pressure, and also highlights the complexity of predator-pathogen interactions. A better understanding of their impact on the gut microbiota and health of marine mussels will help support the sustainability of mussel aquaculture production.

Taxonomic Revision of the Dichotomius mormon (Ljungh, 1799) Species Group (Coleoptera: Scarabaeidae: Scarabaeinae), with a Description of a New Species from Bolivia.

Dichotomius Hope, 1838 (Coleoptera: Scarabaeidae: Scarabaeinae) is a very abundant and diverse genus of dung beetles of the New World ecosystems, with about 190 species, distributed in four subgenera. Luederwaldt (Separata Rev Mus Paul 14: 3-13 1929) proposed the division of subgenera into sections (now species groups) based mainly on characters of external morphology. Based on Luederwaldt's proposal, progress has been made in recent years in the taxonomic revision of the genus; however, inconsistencies have been found in the subgeneric division and species groups proposed by this author. Based on the external morphology and the male genital organ of the all type material and other material deposited in fifteen entomological collections, in this paper, the redefinition and taxonomic revision of the Dichotomius mormon species group is carried out. The new definition of the group and the species key are presented. Five species are included in the group: Dichotomius conicollis (Blanchard, 1846) (Bolivia), Dichotomius larseni sp. nov. (Bolivia), Dichotomius mormon (Ljungh, 1799) (Argentina, Brazil, and Paraguay), Dichotomius ohausi (Luederwaldt, 1923) (Brazil, Colombia, Ecuador, and Peru), and Dichotomius talaus (Erichson, 1847) stat. rev. (Bolivia, and Peru). The lectotypes for D. conicollis, Copris ephialtes Mannerheim, 1829, Copris nasuta Castelnau, 1840, Copris protensus Perty, 1830, D. ohausi, and D. talaus were designated. For each of the species that are included in the group, the following information is presented: taxonomic history, species' citation in published literature, description or redescription of males and females, list of material examined, photographs of the external morphology, illustrations of male genital organ and its endophallites, and distribution map.

‘Altruistic’ cooperation among the prokaryotic community of Atlantic salterns assessed by metagenomics

Hypersaline environments are extreme habitats with a limited prokaryotic diversity, mainly restricted to halophilic or halotolerant archaeal and bacterial taxa adapted to highly saline conditions. This study attempts to analyze the taxonomic and functional diversity of the prokaryotes that inhabit a solar saltern located at the Atlantic Coast, in Isla Cristina (Huelva, Southwest Spain), and the influence of salinity on the diversity and metabolic potential of these prokaryotic communities, as well as the interactions and cooperation among the individuals within that community. Brine samples were obtained from different saltern ponds, with a salinity range between 19.5 % and 39 % (w/v). Total prokaryotic DNA was sequenced using the Illumina shotgun metagenomic strategy and the raw sequence data were analyzed using supercomputing services following the MetaWRAP and SqueezeMeta protocols. The most abundant phyla at moderate salinities (19.5–22 % [w/v]) were Methanobacteriota (formerly “Euryarchaeota”), Pseudomonadota and Bacteroidota, followed by Balneolota and Actinomycetota and Uroviricota in smaller proportions, while at high salinities (36–39 % [w/v]) the most abundant phylum was Methanobacteriota, followed by Bacteroidota. The most abundant genera at intermediate salinities were Halorubrum and the bacterial genus Spiribacter, while the haloarchaeal genera Halorubrum, Halonotius, and Haloquadratum were the main representatives at high salinities. A total of 65 MAGs were reconstructed from the metagenomic datasets and different functions and pathways were identified in them, allowing to find key taxa in the prokaryotic community able to synthesize and supply essential compounds, such as biotin, and precursors of other bioactive molecules, like β-carotene, and bacterioruberin, to other dwellers in this habitat, lacking the required enzymatic machinery to produce them. This work shed light on the ecology of aquatic hypersaline environments, such as the Atlantic Coast salterns, and on the dynamics and factors affecting the microbial populations under such extreme conditions.

Characterization of bacterial diversity in rhizospheric soils, irrigation water, and lettuce crops in municipalities near the Bogotá river, Colombia

The use of wastewater in agricultural practices poses a potential risk for the spread of foodborne diseases. Therefore, this study aimed to characterize the bacterial biodiversity in rhizospheric soil, irrigation water, and lettuce crops in three municipalities adjacent to the Bogotá River, Colombia. Samples were collected in Mosquera, Funza, and Cota municipalities, including rhizospheric soil, lettuce leaves, and irrigation water. The total DNA extraction was performed to analyze bacterial diversity through high-throughput sequencing of the 16S ribosomal RNA genes, utilizing the Illumina HiSeq 2500 PE 300 sequencing platform. A total of 198 genera from the rhizospheric soil were detected including a higher abundance of zOTUs such as Bacillus, Streptomyces, and clinically relevant genera such as Mycobacterium and Pseudomonas. In lettuce, the detection of 26 genera of endophytic bacteria showed to Proteobacteria and Firmicutes as the predominant phyla, with Staphylococcus and Bacillus as the most abundant genera. Notably, Funza's crops exhibited the highest abundance of endophytes, approximately 50 %, compared to Cota (20 %). Furthermore, the most abundant bacterial genera in the irrigation water were Flavobacterium and Pseudomonas. The most prevalent Enterobacteriaceae were Serratia, Enterobacter, Citrobacter, Klebsiella, Yersinia, Shigella, Escherichia, and Erwinia. The Bacillus genus was highly enriched in both rhizospheric soils and lettuce crops, indicating its significant contribution as the main endophytic bacterium.

Biochemical, toxicological and genomic investigation of a high-biomass producing Limnothrix strain isolated from Italian shallow drinking water reservoir

The presence of cyanobacteria in water for drinking and recreational purposes is considered problematic due to their bloom-forming and toxigenic potential. While most cyanotoxins are produced by extensively studied cyanobacteria, little is known about other abundant genera not usually assessed for their toxic potential. Here, a new isolate of Limnothrix redekei from an Italian drinking water reservoir was cultured and investigated using biological, chemical, and genomic methods. Compared to other Limnothrix spp., the isolate yielded high biomass productivity and was mainly constituted by proteins. The isolate had genomic features similar to those of the other 10 genomes of Limnothrix spp. published so far, regardless of their geographical origin. Most genes were implicated in primary metabolism (e.g. photosynthesis, nutrients transport, cell division), while <1 % of the genome was dedicated to secondary metabolism. Two regions encoding for a cyanobactin and a polyketide were found, whereas those for known cyanotoxins were absent. Toxicological investigations based on the crustacean Artemia sp. bioassay revealed potential toxicity of Limnothrix aqueous extracts (mortality >90 %). The highest toxicity was observed in a single fraction of the extract, whose UV spectrum presented carotenoid-like characteristics. Although the structure of the putative toxin was not yet elucidated, these findings pose the basis for further investigations on Limnothrix spp. toxicity, for which the observed toxic aqueous extracts could not exclude possible implications for ecosystems and humans through drinking water resources.

Distribution, community structure and assembly patterns of phytoplankton in the northern South China Sea.

A cruise was conducted in the summer of 2023 from the Pearl River Estuary (PRE) to the adjacent waters of the Xisha Islands in the northern South China Sea (NSCS) to investigate the distribution, community structure, and assembly patterns of eukaryotic and prokaryotic phytoplankton using high-throughput sequencing (HTS) and microscopic observation. Dinophyta were the most abundant phylum in the eukaryotic phytoplankton community based on HTS, accounting for 92.17% of the total amplicon sequence variants (ASVs). Syndiniales was the most abundant order among eukaryotic phytoplankton, whereas Prochlorococcus was the most abundant genus within cyanobacteria. The alpha diversity showed the lowest values in the PRE area and decreased gradually with depth, while cyanobacteria exhibited higher alpha diversity indices in the PRE and at depths ranging from 75 m to 750 m. The morphological results were different from the data based on HTS. Diatoms (37 species) dominated the phytoplankton community, with an average abundance of 3.01 × 104 cells L-1, but only six species of dinoflagellate were observed. Spearman correlation analysis and redundancy analysis (RDA) showed that the distribution and community structure of phytoplankton were largely influenced by geographical location and environmental parameters in the NSCS. The neutral community model (NCM) and null model indicated that deterministic processes played a significant role in the assembly of eukaryotic phytoplankton, with heterogeneous selection and homogeneous selection accounting for 47.27 and 29.95%, respectively. However, stochastic processes (over 60%) dominated the assembly of cyanobacteria and undominated processes accounted for 63.44%. In summary, the formation of eukaryotic phytoplankton was mainly influenced by environmental factors and geographic location, but the assembly of cyanobacteria was shaped by both stochastic processes, which accounted for over 60%, and environmental selection in the NSCS.

A modular toolkit for environmental Rhodococcus, Gordonia, and Nocardia enables complex metabolic manipulation.

Soil-dwelling Actinomycetes are a diverse and ubiquitous component of the global microbiome but largely lack genetic tools comparable to those available in model species such as Escherichia coli or Pseudomonas putida, posing a fundamental barrier to their characterization and utilization as hosts for biotechnology. To address this, we have developed a modular plasmid assembly framework, along with a series of genetic control elements for the previously genetically intractable Gram-positive environmental isolate Rhodococcus ruber C208, and demonstrate conserved functionality in 11 additional environmental isolates of Rhodococcus, Nocardia, and Gordonia. This toolkit encompasses five Mycobacteriale origins of replication, five broad-host-range antibiotic resistance markers, transcriptional and translational control elements, fluorescent reporters, a tetracycline-inducible system, and a counter-selectable marker. We use this toolkit to interrogate the carotenoid biosynthesis pathway in Rhodococcus erythropolis N9T-4, a weakly carotenogenic environmental isolate and engineer higher pathway flux toward the keto-carotenoid canthaxanthin. This work establishes several new genetic tools for environmental Mycobacteriales and provides a synthetic biology framework to support the design of complex genetic circuits in these species.IMPORTANCESoil-dwelling Actinomycetes, particularly the Mycobacteriales, include both diverse new hosts for sustainable biomanufacturing and emerging opportunistic pathogens. Rhodococcus, Gordonia, and Nocardia are three abundant genera with particularly flexible metabolisms and untapped potential for natural product discovery. Among these, Rhodococcus ruber C208 was shown to degrade polyethylene; Gordonia paraffinivorans can assimilate carbon from solid hydrocarbons; and Nocardia neocaledoniensis (and many other Nocardia spp.) possesses dual isoprenoid biosynthesis pathways. Many species accumulate high levels of carotenoid pigments, indicative of highly active isoprenoid biosynthesis pathways which may be harnessed for fermentation of terpenes and other commodity isoprenoids. Modular genetic toolkits have proven valuable for both fundamental and applied research in model organisms, but such tools are lacking for most Actinomycetes. Our suite of genetic tools and DNA assembly framework were developed for broad functionality and to facilitate rapid prototyping of genetic constructs in these organisms.

Causal relationship between gut microbiota and ankylosing spondylitis and potential mediating role of inflammatory cytokines: A mendelian randomization study.

Associations between gut microbiota and ankylosing spondylitis have been discovered in previous studies, but whether these associations reflect a causal relationship remains inconclusive. Aiming to reveal the bidirectional causal associations between gut microbiota and ankylosing spondylitis, we utilized publicly available genome wide association study summary data for 211 gut microbiota (GM) taxa and ankylosing spondylitis (AS) to conduct two sample mendelian randomization analyses. Mediation analysis was performed to explore mediating inflammatory cytokines. We found that genetically predicted higher abundance of Lactobacillaceae family, Rikenellaceae family and Howardella genus had suggestive associations with decreased risk of ankylosing spondylitis while genetic proxied higher abundance of Actinobacteria class and Ruminococcaceae_NK4A214_group genus was associated with increased risk of ankylosing spondylitis. IL23 and IFN-γ were potential mediating cytokines for GM dysbiosis, especially for Actinobacteria class, leading to AS. Our study provided a new exploration direction for the treatment of AS. Lactobacillaceae family, Rikenellaceae family, Howardella genus, Actinobacteria class and Ruminococcaceae_NK4A214_group genus are expected to become new therapeutic targets and monitoring indicators for AS.

Correlation between the Characteristic Flavour and Microbial Community of Xuanwei Ham after Ripening

Xuanwei ham is a traditional fermented meat product in China with a unique production process and excellent-quality reputation at home and abroad. To reveal the microbial community succession of Xuanwei ham at different post-ripening times (W1-4) and its relationship with flavour formation, the microbial community, free amino acids, and volatile flavour compounds (VOCs) were analysed by high-throughput sequencing, liquid chromatography (LC), and gas chromatography–mass spectrometry (GC-MS), respectively. A total of 25 free amino acids were detected, among which W3 contained the fewest, and most were generally lower than in hams in the other three years. Fifty-nine VOCs were detected, among which 17 were esters, and the highest ester content was found in W4. Analysis of the bacterial community composition revealed that the bacterial community composition of ham samples from W3 and other years differed greatly, and at the gate level, the dominant bacterial group of Xuanwei ham from different years was Pseudomonadota. At the genus level, the most abundant genera in W1, W2, and W4 were all dominated by Sarocladium, Klebsiella, and Vibrio, with Klebsiella being the most abundant in W1. The most abundant genus in W3 was Vibrio, and the second most dominant genera were Sarocladium and Gammaretrovirus. In short, this study provides a theoretical basis for the storage, quality, and improvement of Xuanwei ham.

Deciphering the gut microbiota of zebrafish, the most used fish as a biological model: A meta-analytic approach

A meta-analytic approach deciphered the taxonomic profile of the zebrafish gut microbiota at different developmental stages. Data (16S rDNA) were systematically searched in databases, selecting those with intestine samples of fish not exposed to a particular treatment or challenge (e.g., pathogens, dietetic tests, xenobiotics, etc.) and obtaining 340 samples to be processed. Results revealed marked differences between the developmental phases. Proteobacteria was the dominant phylum in the larval phase, with a relative abundance of 90%, while the rest of the phyla did not exceed 2%. Vibrio, Aeromonas, Plesiomonas, Pseudomonas, Shewanella, and Acinetobacter were the dominant genera in this phase. Transitional changes were observed after the larvae stage. Proteobacteria still registered high abundance (48%) in the juvenile phase, but Fusobacteria (40%) and Bacteriodota (5.9%) registered considerable increases. Genera, including Cetobacterium, Plesiomonas, Aeromonas, Vibrio, and Flavobacterium, dominated this stage. The phyla Proteobacteria (48%) and Fusobacteria (35%) were strongly established in the adult phase. Cetobacterium was registered as the most abundant genus, followed by Aeromonas, Acinetobacter, Plesiomonas, Vibrio, and ZOR0006 (Firmicutes; 6%). In conclusion, the composition of the intestinal microbiota of zebrafish is consistently determined by two primary phyla, Proteobacteria and Fusobacteria; however, this composition varies depending on the developmental stage. Cetobacterium and Aeromonas are the most relevant genera in juveniles and adults. Finally, these results reveal a consistent pattern of certain bacterial groups in the zebrafish microbiota that could help shape gnotobiotic models (colonized with a specific known bacterial community) or synthetic microbiota (in vitro assembly of microbes), among other approaches.