16S rRNA High-throughput Sequencing Research Articles

Multicompartmental traumatic injury and the microbiome: Shift to a pathobiome.

Previous animal models have demonstrated altered gut microbiome after mild traumatic injury; however, the impact of injury severity and critical illness is unknown. We hypothesized that a rodent model of severe multicompartmental injuries and chronic stress would demonstrate microbiome alterations toward a "pathobiome" characterized by an overabundance of pathogenic organisms, which would persist 1 week after injury. Male Sprague-Dawley rats (n = 8 per group) were subjected to either multiple injuries (PT) (lung contusion, hemorrhagic shock, cecectomy, and bifemoral pseudofractures), PT plus daily chronic restraint stress for 2 hours (PT/CS), or naive controls. Fecal microbiome was measured on days 0, 3, and 7 using high-throughput 16S rRNA sequencing and Quantitative Insights Into Microbial Ecology 2 bioinformatics analysis. Microbial α diversity was assessed using Chao1 and Shannon indices, and β diversity with principle coordinate analysis. Intestinal permeability was evaluated by plasma occludin; ileum and descending colon tissues were reviewed for injury. Analyses were performed in GraphPad (GraphPad Software, La Jolla, CA) and R (R Foundation for Statistical Computing, Vienna, Austria), with significance defined as p < 0.05. There were significant alterations in β diversity at day 3 and between all groups. By day 3, both PT and PT/CS demonstrated significantly depleted bacterial diversity (Chao1) ( p = 0.01 and p = 0.001, respectively) versus naive, which persisted up to day 7 in PT/CS only ( p = 0.001). Anaerostipes and Rothia dominated PT and Lactobacillus bloomed in PT/CS cohorts by day 7. Plasma occludin was significantly elevated in PT/CS compared with naive ( p = 0.04), and descending colon of both PT and PT/CS showed significantly higher injury compared with naive ( p = 0.005, p = 0.006). Multiple injuries with and without chronic stress induces significant alterations in microbiome diversity and composition within 3 days; these changes are more prominent and persist for 1 week postinjury with stress. This rapid and persistent transition to a "pathobiome" phenotype represents a critical phenomenon that may influence outcomes after severe trauma and critical illness.

EXPLORING THE BACTERIAL COMMUNITY IN THE SEDIMENTS OF AN ANTHROPICALLY POLLUTED URBAN CREEK LOCATED ON THE WEST COAST OF MUMBAI, INDIA

Microbial communities with their key roles in nutrient cycling and degradation of pollutants aresuitable bio-indicators in gauging the health of a marine ecosystem. However, insights into thestructure and diversity of bacterial communities in sediments of Versova creek of Mumbai arelacking. Here we assessed the bacterial diversity and composition in sediments collected from twosampling stations for two months in Versova creek. The total sediment DNA was extracted andsubjected to high throughput 16S rRNA sequencing technology which resulted in a total of 5467unique OTUs (Operational Taxonomic Units) from four samples. 16S rRNA sequences revealed thedominance of phyla Proteobacteria, Bacteriodetes, Tenericutes, Chloroflexi and Firmicutes. Furthertaxonomic analysis revealed the surface sediments to be abundant in sulfate reducing taxaDeltaproteobacteria (Desulfobacteraceae, Desulfobulbaceae and Desulfarculaceae). Organic matterloading and oxygen availability could be one of the prime factors affecting the bacterialcommunity structure in the sediments of Versova creek. Additionally, except for Nickel andCopper, which surpassed the toxic thresholds set by international sediment quality standards, theconcentration of most select heavy metals in the creek sediments revealed a moderate level ofcontamination. This study provides preliminary evidence of pollution in Versova creek due torelease of contaminants beyond the assimilative capacity of the ecosystem. It provides a baselineassessment that can be used as a benchmark for future studies and policies that needs to bedeployed in restoring the health of this system.

Transformation of dissolved organic matter in landfill leachate during a membrane bioreactor treatment

In this study, a cutting-edge mass spectrometry (MS) technique, Orbitrap fusion MS with ultrahigh resolution, was used to analyze the molecular composition, chemical properties, formation mechanism, and environmental impact of refractory dissolved organic matter (rDOM) in leachate. The results showed that the bioavailable DOM (bDOM) and rDOM constituents varied substantially during the biological treatment of landfill leachate. Compared with bDOM, the rDOM in leachate had a higher degree of unsaturation, aromaticity, and oxidation, and a larger molecular weight, and contained more organic matter with benzene ring and biphenyl structures. Using high-throughput 16S rRNA sequencing, metagenomics, the Kendrick mass defect (KMD), and a mass difference network (MDiN), it was found that rDOM in leachate is generated through carboxylation (+COO), dehydro-oligomerization (-H2), and chain scission (-CH2) pathways due to the activity of microbes such as Patescibacteria, Chloroflexi, and Proteobacteria. Compared with Suwannee River fulvic acid (SRFA), the rDOM in leachate contained more organics with nitrogen, sulfur, benzene rings, and biphenyls. If the rDOM in leachate enters the environment it will affect the composition of the original organic matter, and its biogeochemical transformation and environmental fate will then need to be monitored and may require special attention.

Intestinal microbial diversity in female rhesus (Macaca mulatta) at different physiological periods.

To explore the relationship between the changes in the physiological period and the fecal microbial population of female rhesus monkeys by measuring microbial composition of fecal samples and the serum hormones. Blood and fecal samples were collected from six female adult rhesus monkeys during the menstrual period (MP), ovulation period (OP), and Luteal period (LP). Serum estradiol (E2) and progesterone (P) levels were determined by the chemiluminescence method and the stool samples were subjected to high-throughput 16S rRNA sequencing. The highest level of E2 and P secretions were during the MP, and LP, respectively. Stool samples produced valid sequences and the number of operational taxonomic unit/OTU was: 810056/3756 (MP), 845242/4159 (OP), 881560/3970 (LP). At the phylum level, the three groups of Firmicutes and Bacteroides accounted for > 95%. The dominant flora at the LP was Bacteroides (53.85%), the dominant flora at the MP and OP was Firmicutes, 64.08 and 56.53%, respectively. At the genus level, the dominant genus at the LP was Prevotella, the dominant genera at the MP were Prevotella, Oncococcus, Streptococcus, and Kurtella. The dominant genera at OP were Prevotella and Nocococcus. At the phylum level, P levels were negatively correlated to Firmicutes, Actinomycetes Actinobacteria, and Fibrobacteres, but positively correlated to Bacteroidetes. Likewise, E2 was positively correlated to Proteobacteria but negatively correlated to Euryarchaeota. At the genus level, P hormone showed a significant correlation with 16 bacterial species, and E2 was significantly correlated to seven bacterial species. Function prediction analysis revealed a high similarity between the MP and OP with six differentially functional genes (DFGs) between them and 11 DFGs between OP and LP (P < 0.05). Fecal microbiota types of female rhesus monkeys varied with different stages of the menstrual cycle, possibly related to changes in hormone levels.

Effects of fecal microbiota transplantation from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein calves.

This study was conducted to investigate the effect of fecal microbiota transplantation (FMT) from yaks on weaning diarrhea, fecal microbiota composition, microbial network structure and functional pathways in Chinese Holstein Calves. In this study, 50 calves were randomly divided into five groups of 10 each: NC group (no supplementation), Control group (normal saline), low concentration FMT group (LFMT, 1 × 108 CFU/ml), high concentration FMT group (HMFT, 1 × 109 CFU/ml), and sterilized FMT group (SMFT, sterilized bacterial solution). The test lasted for 30 days. We found that FMT reduced the incidence of diarrhea in weaned calves, and the anti-diarrhea effect of LFMT was stronger than those of HFMT and SFMT. Calf feces were collected by rectal palpation on days 5, 10, 15, and 20 post-weaning, and high-throughput sequencing of bacterial 16S rRNA and fungal internal transcribed spacer region of fecal microbiota was performed. We observed that the richness and diversity of bacterial microbiota in the LFMT, HFMT, and SFMT groups were higher than those in the NC and Control groups at day 20 after weaning. The treatment had a significant effect on bacterial richness (p < 0.05), but not on fungal diversity or richness. The analysis of gut microbiome showed that Firmicutes and Bacteroides were the main bacterial phyla in the feces of weaned calves, and norank_ f Muribaculaceae, UCG-005, Rikenellaceae_RC9_gut_group, Bacteroides, and Blautia were the main genera. Ascomycota and Basidiomycota were the main fungal phyla. Compared to abundance parameters in the Control and NC groups, relative abundances of Firmicutes in the FMT groups increased at different time points after weaning. The relative abundance of Blautia and Lactobacillus in the LFMT group increased significantly after weaning. In addition, abundances of Ruminococcus and Romboutsia, which produce short-chain fatty acids, were also increased in different FMT groups. FMT significantly increased the relative abundance of beneficial bacteria, enhanced the complexity of the fecal microbial network, and promoted important metabolic and cellular processes in weaned calves. In conclusion, our study provides a reference and theoretical basis for FMT to prevent calf weaning diarrhea and other intestinal diseases in ruminants.

Comparison of tumor-associated and nontumor-associated esophageal mucosa microbiota in patients with esophageal squamous cell carcinoma.

Esophageal microbiota plays important roles in esophageal squamous cell carcinoma (ESCC). The aims of this study were to clarify the changes in the bacterial community during ESCC development and identify latent pathogenic bacteria which may contribute to esophageal carcinogenesis and progression. Fresh tumor and nontumor esophageal mucosal samples were collected from 31 men with ESCC. High-throughput 16s rRNA sequencing was performed, and the operational taxonomic unit data and bacterial classification annotation were obtained and analyzed. The Ace, Chao, Shannon, Simpson indexes, and operational taxonomic unit numbers were higher in nontumor tissues than in tumor tissues, although without statistical significance. There were 4 phyla and 28 genera found to show significant differences between tumor and nontumor samples. The general probiotic Lactobacillus was 1.98-fold higher in nontumor tissues, while the general pathogenic genera Fusobacterium was 4.35-fold higher in tumor tissues. For tumor tissue samples, the genera Treponema and Brevibacillus were significantly higher in N1 and N2 stages, respectively, and Acinetobacter was significantly higher in T3 stage. For nontumor tissues, the genus Fusicatenibacter was significantly higher in T2 stage, and Corynebacterium, Aggregatibacter, Saccharimonadaceae-TM7x, and Cupriavidus were significantly higher in T4 stage. Additionally, bacteria related to nitrotoluene degradation were enriched in nontumor tissues, while bacteria related to base excision repair were enriched in tumor tissues. The relative abundance of several phyla and genera are different between tumor and nontumor tissue samples. The altered bacterial microbiota is correlated with different tumor stages and some microbes may take part in the carcinogenesis and development of ESCC.

The emerging pathogen Enterocytozoon hepatopenaei drives a degenerative cyclic pattern in the hepatopancreas microbiome of the shrimp (Penaeus vannamei)

The microsporidian Enterocytozoon hepatopenaei (EHP) is an emerging pathogen that causes substantial economic losses in shrimp (Penaeus spp.) aquaculture worldwide. To prevent diseases in shrimp, the manipulation of the gut microbiota has been suggested. However, prior knowledge of the host-microbiome is necessary. We assessed the modulation of the microbiome (bacteria/fungi) and its predicted functions over the course of disease progression in shrimp experimentally challenged with EHP for 30 days using high throughput 16S rRNA and ITS amplicon sequencing. Infection grade was assessed for the first time by quantitative digital histopathology. According to the infection intensity, three disease-stages (early/developmental/late) were registered. During the early-stage, EHP was not consistently detected, and a high diversity of potentially beneficial microorganisms related to nutrient assimilation were found. In the development-stage, most of the shrimp start to register a high infection intensity related to a decrease in beneficial microorganisms and an increase in opportunistic/pathogenic fungi. During late-stage, animals displayed different infection intensities, showed a displacement of beneficial microorganisms by opportunistic/pathogenic bacteria and fungi related to pathogen infection processes and depletion of energetic reserves. The degenerative cyclic pattern of EHP infection and its effects on beneficial microorganisms and beneficial functions of the shrimp hepatopancreas microbiome are discussed.

The beneficial effects of Polygonatum sibiricum Red. superfine powder on metabolic hypertensive rats via gut-derived LPS/TLR4 pathway inhibition

BackgroundMetabolic hypertension (MH) is characterized by elevated blood pressure accompanied by metabolic abnormalities, with the gut-derived lipopolysaccharide/toll like receptor 4 (LPS/TLR4) pathway an important triggering mechanism. The conventional Chinese plant Polygonatum sibiricum Red. is traditionally used as a medicinal and edible food source. Currently, several studies have examined its anti-obesity and anti-diabetic actions, with potential roles for MH treatment; however, specific P. sibiricum Red. roles in MH and associated mechanisms remain unclear. ObjectivesOur purpose was to identify the effects and mechanisms of P. sibiricum Red. superfine powder (PSP) in a MH rat model triggered by high sugar and high fat compounds in an excessive alcohol diet (ACHSFDs). MethodsA MH rat model was induced by ACHSFDs, and PSP was administered daily at 0.5 and 1.0 g/kg doses, respectively. Firstly, the effects of PSP on MH were assessed using blood pressure, serum lipid, and lipid deposition assays in the liver. Changes in intestinal flora were detected by high-throughput 16S rRNA sequencing, while metabolite short-chain fatty acids (SCFAs) and LPS levels were quantified by gas chromatography (GC) and enzyme-linked immunosorbent assay (ELISA), respectively. Hematoxylin & eosin (H&E) staining and transmission electron microscopy (TEM) were performed to evaluate histopathological changes in the rat colon. d-lactic acid (d-LA) levels and tight junction proteins (TJPs) expression were also measured to assess intestinal barrier function. Also, aortic endothelial microstructures, serum endothelin 1 (ET-1), and nitric oxide (NO) levels were investigated to determine vascular endothelial function. Finally, the TLR4/MyD88 signaling pathway in the aorta and gut was evaluated by western blotting, immunohistochemistry (IHC), and quantitative real-time polymerase chain reaction (qRT-PCR). ResultsBlood pressure and blood lipid metabolism disorders induced by ACHSFDs in MH rats were improved by PSP administration. Intestinal flora analyses revealed decreased SCFAs and LPS levels following PSP administration, which was accompanied by increased Streptococcus species levels and decreased Desulfobacter and Desulfovibrio species levels. PSP increased SCFAs levels, and the expression of SCFAs receptors GPCR41 and GPCR43 in the colon. Meanwhile, the expression of tight junction proteins (TJPs) such as Claudin-1, occludin were upregulated in the ileum and colon, while TLR4 and MyD88 were downregulated, thereby strengthening intestinal barrier integrity and reducing serum LPS levels. Additionally, PSP treatment improved vascular endothelial function by inhibiting the TLR4/MyD88 pathway in vessels, improving vascular endothelial cell shedding, and regulating the NO and ET-1 balance. ConclusionsWe demonstrated the beneficial effects and potential mechanisms of PSP in our MH rat model. Based on gut microbiota structure modulation and intestinal barrier improvements, PSP inhibited LPS-induced vascular TLR4/MyD88 signaling activation to improve vascular endothelial function, which in turn reduced blood pressure. Our study provides valuable insights on PSP therapy for MH.

The Association between Gut Microbiome Diversity and Composition and Heat Tolerance in Cattle.

Cattle are raised around the world and are frequently exposed to heat stress, whether in tropical countries or in regions with temperate climates. It is universally acknowledged that compared to those in temperate areas, the cattle breeds developed in tropical and subtropical areas have better heat tolerance. However, the underlying mechanism of heat tolerance has not been fully studied, especially from the perspective of intestinal microbiomics. The present study collected fecal samples of cattle from four representative climatic regions of China, namely, the mesotemperate (HLJ), warm temperate (SD), subtropical (HK), and tropical (SS) regions. Then, the feces were analyzed using high-throughput 16S rRNA sequencing. The results showed that with increasing climatic temperature from HLJ to SS, the abundance of Firmicutes increased, accompanied by an increasing Firmicutes to Bacteroidota ratio. Proteobacteria showed a trend of reduction from HLJ to SS. Patescibacteria, Chloroflexi, and Actinobacteriota were particularly highest in SS for adapting to the tropical environment. The microbial phenotype in the tropics was characterized by an increase in Gram-positive bacteria and a decrease in Gram-negative bacteria, aerobic bacteria, and the forming of_biofilms. Consistently, the functional abundances of organismal systems and metabolism were decreased to reduce the material and energy demands in a hot environment. Genetic information processing and information storage and processing may be how gut flora deals with hot conditions. The present study revealed the differences in the structure and function of gut microbes of cattle from mesotemperate to tropical climates and provided an important reference for future research on the mechanism of heat tolerance regulated by the gut microbiota and a potential microbiota-based target to alleviate heat stress.

Exploring Core Microbiota Based on Characteristic Flavor Compounds in Different Fermentation Phases of Sufu.

Sufu, a Chinese traditional fermented soybean product, has a characteristic foul smell but a pleasant taste. We determined the core functional microbiota and their metabolic mechanisms during sufu fermentation by examining relationships among bacteria, characteristic flavor compounds, and physicochemical factors. Flavor compounds in sufu were detected through headspace solid-phase microextraction coupled with gas chromatography–mass spectrometry, and the microbial community structure was determined through high-throughput 16S rRNA sequencing. The results showed that the fermentation process of sufu could be divided into early and late stages. The early stage was critical for flavor development. Seven microbiota were screened based on their abundance, microbial relevance, and flavor production capacity. Five microbes were screened in the early stage: Pseudomonas, Tetragenococcus, Lysinibacillus, Pantoea, and Burkholderia–Caballeronia–Paraburkholderia. Three microbes were screened in the late stage: Exiguobacterium, Bacillus, and Pseudomonas. Their metabolic profiles were predicted. The results provided a reference for the selection of enriched bacterial genera in the fermentation process and controlling applicable process conditions to improve the flavor of sufu.

Slower antibiotics degradation and higher resistance genes enrichment in plastisphere

Microplastics (MPs) are increasingly entering the urban aquatic ecosystems, and the environmental significance and health risks of plastisphere, a special biofilm on MPs, have received widespread attention. In this study, MPs of polylactic acid (PLA) and polyvinyl chloride (PVC) and quartzite were incubated in an urban water environment, and the tetracycline (TC) degradation ability was compared. Approximatedly 24% of TC biodegraded in 28 d in the water-quartzite system, which is significantly higher than that in the water-PLA (17.3%) and water-PVC systems (16.7%). Re-incubation of microorganisms in biofilms affirmed that quartzite biofilm has a higher TC degradation capacity than the plastisphere. According to high-throughput sequencing of 16S rRNA and metagenomic analysis, quartzite biofilm contained more abundant potential TC degrading bacteria, genes related to TC degradation (eutG, aceE, and DLAT), and metabolic pathways related to TC degradation. An oligotrophic environment on the quartzite surface might lead to the higher metabolic capacity of quartzite biofilm for unconventional carbons, e.g., TC. It is also found that, compared with quartzite biofilm, the distinct microbes in the plastisphere carried more antibiotic resistance genes (ARGs). Higher affinity of MPs surface to antibiotics may lead to higher antibiotics stress on the plastisphere, which further amplify the carrying capacity for ARGs of microorganisms in the plastisphere. Compared to the nondegradable PVC MPs, surface of the biodegradable PLA plastics harbored significantly higher amounts of biomass and ARGs. Compared to the mineral particles, the capability of plastisphere has lower ability to degrade unconventional carbon sources such as the refractory organic pollutants, due to the abundance of carbon sources (adsorbed organic carbon and endogenous organic carbon) on the MPs surface. Meanwhile, the stronger adsorption capacity for pollutants also leads to higher pollutant stress (such as antibiotic stress) in plastisphere, which in turn affects the microbiological characteristics of the plastisphere itself, such as carrying more ARGs.

Influence of planting methods and organic amendments on rice yield and bacterial communities in the rhizosphere soil.

A comprehensive understanding of rice cultivation techniques and organic amendments affecting soil quality, enzyme activities and bacterial community structure is crucial. We investigated two planting methods (direct seeding and transplanting) of paddy rice (Oryza sativa) and organic amendments with rice straw and biochar on crop yield and soil biological and physicochemical properties. Rhizosphere bacterial communities at the maturity stage of rice growth were characterized through high-throughput 16S rRNA sequencing. Soil biochemical properties and enzyme activity levels were analyzed. Grain yield of paddy rice with transplanting increased 10.6% more than that with direct seeding. The application of rice straw increased grain yield by 7.1 and 8.2%, more than with biochar and the control, respectively. Compared to biochar and the control, the application of rice straw significantly increased sucrase, cellulase, protease, organic carbon, available phosphorus, nitrate, and ammonium. The application of biochar increased microbial biomass nitrogen and carbon, urease, pH, available nitrogen, and available potassium compared to the application of rice straw and the control. Principal coordinate analysis and dissimilarity distances confirmed significant differences among the microbial communities associated with planting methods and organic amendments. Bacteroidetes, Nitrospirae, Firmicutes, and Gemmatimonadetes abundance increased with rice straw relative to biochar and the control. The biochar addition was associated with significant increases in Chloroflexi, Patescibacteria, Proteobacteria, and Actinobacteria abundance. Pearson’s correlation analyzes showed that Chloroflexi, Bacteroidetes and Nitrospirae abundance was positively correlated with grain yield. The relative abundance of these bacteria in soil may be beneficial for improving grain yield. These results suggest that planting methods and organic amendments impact soil biochemical characteristics, enzyme activity levels, and microbial community composition.

Biogas slurry application alters soil properties, reshapes the soil microbial community, and alleviates root rot of Panax notoginseng.

BackgroundPanax notoginseng is an important herbal medicine in China, where this crop is cultivated by replanting of seedlings. Root rot disease threatens the sustainability of P. notoginseng cultivation. Water flooding (WF) is widely used to control numerous soilborne diseases, and biogas slurry shows positive effects on the soil physiochemical properties and microbial community structure and has the potential to suppress soilborne pathogens. Hence, biogas slurry flooding (BSF) may be an effective approach for alleviating root rot disease of P. notoginseng; however, the underlying mechanism needs to be elucidated.MethodsIn this study, we conducted a microcosm experiment to determine if BSF can reduce the abundance of pathogens in soil and, alleviate root rot of P. notoginseng. Microcosms, containing soil collected from a patch of P. notoginseng showing symptoms of root rot disease, were subjected to WF or BSF at two concentrations for two durations (15 and 30 days), after which the changes in their physicochemical properties were investigated. Culturable microorganisms and the root rot ratio were also estimated. We next compared changes in the microbial community structure of soils under BSF with changes in WF and untreated soils through high-throughput sequencing of bacterial 16S rRNA (16S) and fungal internal transcribed spacer (ITS) genes amplicon.ResultsWF treatment did not obviously change the soil microbiota. In contrast, BSF treatment significantly altered the physicochemical properties and reshaped the bacterial and fungal communities, reduced the relative abundance of potential fungal pathogens (Fusarium, Cylindrocarpon, Alternaria, and Phoma), and suppressed culturable fungi and Fusarium. The changes in the microbial community structure corresponded to decreased root rot ratios. The mechanisms of fungal pathogen suppression by BSF involved several factors, including inducing anaerobic/conductive conditions, altering the soil physicochemical properties, enriching the anaerobic and culturable bacteria, and increasing the phylogenetic relatedness of the bacterial community.ConclusionsBSF application can reshape the soil microbial community, reduce the abundance of potential pathogens, and alleviate root rot in P. notoginseng. Thus, it is a promising practice for controlling root rot disease in P. notoginseng.

Impacts of light on gut microbiota in Chinese mitten crab (Eriocheir sinensis)

ABSTRACT Photoperiod is an essential environmental factor that affects physiological activity and feeding behavior in crustaceans. The current study aimed to investigate the mechanism by which photoperiod influences gut bacterial community composition in the Chinese mitten crab (Eriocheir sinensis). In this study, high-throughput 16S rRNA sequencing was used to identify variations in E. sinensis gut bacteria under three different light: dark conditions (24 L:0 D, 0 L:24 D, and 12 L:12 D). Shannon and Chao1 indexes of community richness and diversity differed significantly between the complete light group and complete dark group on day 4, but these differences disappeared by day 6, suggesting that the gut bacterial community became disrupted on day 4, but adjusted to the new environment by day 6. Tenericutes and Proteobacteria were the dominant phyla under all conditions. Clostridium abundance increased significantly on day 6 under conditions of complete light and complete darkness. These data suggest that the biological clock of E. sinensis minimized changes in gut bacterial community composition under different light conditions. Considering that the gut bacterial community has profound effects on the host, understanding various mechanisms of its influence (including interactions with photoperiod) should be useful for improving E. sinensis aquaculture.

The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota.

For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.

The Characterization of Microbiome and Interactions on Weathered Rocks in a Subsurface Karst Cave, Central China

Karst caves are a natural oligotrophic subsurface biosphere widely distributed in southern China. Despite the progress in bacterial and fungal diversity, the knowledge about interactions between bacteria, fungi, and minerals is still limited in caves. Hence, for the first time, we investigated the interaction between bacteria and fungi living on weathered rocks in the Heshang Cave via high-throughput sequencing of 16S rRNA and ITS1 genes, and co-occurrence analysis. The mineral compositions of weathered rocks were analyzed by X-ray diffraction. Bacterial communities were dominated by Actinobacteria (33.68%), followed by Alphaproteobacteria (8.78%), and Planctomycetia (8.73%). In contrast, fungal communities were dominated by Sordariomycetes (21.08%) and Dothideomycetes (14.06%). Mineral substrata, particularly phosphorus-bearing minerals, significantly impacted bacterial (hydroxyapatite) and fungal (fluorapatite) communities as indicated by the redundancy analysis. In comparison with fungi, the development of bacterial communities was more controlled by the environmental selection indicated by the overwhelming contribution of deterministic processes. Co-occurrence network analysis showed that all nodes were positively linked, indicating ubiquitous cooperation within bacterial groups and fungal groups, as well as between bacteria and fungi under oligotrophic conditions in the subsurface biosphere. In total, 19 bacterial ASVs and 34 fungal OTUs were identified as keystone taxa, suggesting the fundamental role of fungi in maintaining the microbial ecosystem on weathered rocks. Ascomycota was most dominant in keystone taxa, accounting for 26.42%, followed by Actinobacteria in bacteria (24.53%). Collectively, our results confirmed the highly diverse bacterial and fungal communities on weathered rocks, and their close cooperation to sustain the subsurface ecosystem. Phosphorus-bearing minerals were of significance in shaping epipetreous bacterial and fungal communities. These observations provide new knowledge about microbial interactions between bacteria, fungi, and minerals in the subterranean biosphere.

The Shift of Soil Bacterial Community After Afforestation Influence Soil Organic Carbon and Aggregate Stability in Karst Region.

Soil microbes regulate the carbon cycle and affect the formation and stabilization of soil aggregates. However, the interactions between the soil microbial community and soil organic carbon (SOC) fractions, organic carbon (OC) content in aggregates, and soil aggregate stability after afforestation are remain poorly understood. In our study, we investigated SOC fractions in bulk soil, aggregate-associated OC content, soil aggregate stability, and soil bacterial community with high-throughput 16S rRNA sequencing at sites representing natural secondary forest (NF) and managed forest (MF), with cropland (CL) as reference in a degraded karst region of Southwest China. Our results showed that afforestation remarkably increased the SOC fraction and OC content in aggregates, the mean weight diameter (MWD), and the mean geometric diameter (GMD). The most dominant bacterial phyla detected were Acidobacteriota, Actinobacteriota, Proteobacteria, and Chloroflexi across all soils. Afforestation remarkably altered the relative abundances of most of the dominant soil bacteria at the phylum, class, and order levels. Interestingly, such changes in the abundance of soil bacteria taxa had significantly effects on SOC fraction, aggregate-associated OC content, MWD, and MGD. The abundance of dominant bacterial taxa such as Methylomirabilota, Latescibacterota, Methylomirabilia, MB-A2-108, norank_Latescibacterota; Dehalococcoidia, Rokubacteriales, Gaiellales, Microtrichales, norank_c__MB-A2-108, norank_c__norank_p__Latescibacterota, Rhizobiales, and S085 not only remarkably increased but also had significant positive effects on SOC fractions and aggregate-associated OC content after afforestation. Moreover, MWD and MGD were positively correlated with the relative abundance of Methylomirabilota, Methylomirabilia, Rokubacteriales, Latescibacterota, and Rhizobiales. Results indicated the importance of certain soil bacteria for regulating SOC storage and soil aggregate stability. We concluded that afforestation on cropland could alter the abundance of soil bacteria, and these changes modulate the stability of soil aggregates and SOC fractions.

Increased number of children in households may protect against inflammatory bowel disease.

The increasing incidence of inflammatory bowel disease (IBD: Crohn's disease and ulcerative colitis) around the world has coincided with a wide array of environmental and epidemiologic changes. The relationship between IBD incidence and household or family size decline, however, has not been examined before. Our background epidemiological analyses suggested an inverse association between household size and IBD incidence. We aimed to examine this further in a murine model. We designed a unique two-generation cohousing model of family size and IBD susceptibility in C57BL/6J mice. Serial fecal microbiomes during cohousing were examined by high-throughput 16S rRNA sequencing. After cohousing for 10 days, mice were exposed to dextran sulfate sodium (DSS) to induce acute colitis. Body weight as a significant correlate of colitis severity was measured. Mice in a large household arrangement demonstrated less weight loss than mice in the small household arrangement in the DSS model. Age- and housing-dependent microbiome shifts were found. Larger households may be protective against intestinal inflammation through intergenerational microbiome modulation. Our observations may set the foundation for age-dependent, microbiome-directed future prevention against IBD. Epidemiological analyses in this study suggested that IBD incidence may inversely correlate with household size (an indicator of family size/children per family), which has not been examined before. A uniquely designed two-generation cohousing model of family size and IBD susceptibility in mice supported our epidemiologic observations. Microbiome changes in our cohousing model may set the foundation for age-dependent, microbiome-directed prevention against IBD.

Organic mulch can suppress litchi downy blight through modification of soil microbial community structure and functional potentials

BackgroundOrganic mulch is an important management practice in agricultural production to improve soil quality, control crop pests and diseases and increase the biodiversity of soil microecosystem. However, the information about soil microbial diversity and composition in litchi plantation response to organic mulch and its attribution to litchi downy blight severity was limited. This study aimed to investigate the effect of organic mulch on litchi downy blight, and evaluate the biodiversity and antimicrobial potential of soil microbial community of litchi plantation soils under organic mulch.ResultsOrganic mulch could significantly suppress the disease incidence in the litchi plantation, and with a reduction of 37.74% to 85.66%. As a result of high-throughput 16S rRNA and ITS rDNA gene illumine sequencing, significantly higher bacterial and fungal community diversity indexes were found in organic mulch soils, the relative abundance of norank f norank o Vicinamibacterales, norank f Vicinamibacteraceae, norank f Xanthobacteraceae, Unclassified c sordariomycetes, Aspergillus and Thermomyces were significant more than that in control soils. Isolation and analysis of antagonistic microorganism showed that 29 antagonistic bacteria strains and 37 antagonistic fungi strains were unique for mulching soils.ConclusionsThus, we believe that organic mulch has a positive regulatory effect on the litchi downy blight and the soil microbial communities, and so, is more suitable for litchi plantation.

An emerging unrated mobile reservoir for antibiotic resistant genes: Does transportation matter to the spread

The regional distribution of antibiotic resistance genes has been caused by the use and preference of antibiotics. Not only environmental factors, but also the population movement associated with transportation development might have had a great impact, but yet less is known regarding this issue. This research study has investigated and reported that the high-speed railway train was a possible mobile reservoir of bacteria with antibiotic resistance, based on the occurrence, diversity, and abundance of antibiotic resistant bacteria (ARB), antibiotic resistance genes (ARGs), and mobile gene elements (MGEs) in untreated train wastewater. High-throughput 16S rRNA sequencing analyses have indicated that opportunistic pathogens like Pseudomonas and Enterococcuss were the predominant bacteria in all samples, especially in cultivable multi-antibiotic resistant bacteria. The further isolated Enterococcus faecalis and Enterococcus faecium exhibited multi-antibiotic resistance ability, potentially being an indicator for disinfection proficiency. Positive correlations amongst ARGs and MGEs were observed, such as between intI1 and tetW, tetA, blaTEM, among Tn916/154 and mefA/F, qnrS, implying a broad dissemination of multi-ARGs during transportation. The study findings suggested that the high-speed railway train wastewater encompassed highly abundant antibiotic-resistant pathogens, and the wastewater discharge without effective treatment may pose severe hazards to human health and ecosystem safety.