High-throughput 16S rRNA Gene Sequencing Research Articles

Comprehensive profiling and risk assessment of antibiotic resistance genes in a drinking water watershed by integrated analysis of air-water-soil

The prevalence of antibiotic resistance genes (ARGs) in diverse habitats threatens public health. Watersheds represent critical freshwater ecosystems that interact with both the soil and atmosphere. However, a holistic understanding of ARGs distribution across these environmental media is currently inadequate. We profiled ARGs and bacterial communities in air-water-soil in the same watershed area during four seasons using high-throughput qPCR and 16S rRNA gene sequencing. Our findings demonstrated that aminoglycoside resistance genes (58.5%) were dominant in water, and multidrug resistance genes (55.2% and 54.2%) were dominant in soil and air. Five ARGs and nineteen bacterial genera were consistently detected in all samples, were named as shared genes or bacteria. Co-occurrence Network analysis revealed the co-occurrence module of resistance genes, mobile genetic elements (MGEs), and potential bacterial hosts, indicating that shared genes and bacteria may persist and co-spread across different environmental media. The risk assessment framework, based on ARGs’ abundance, detection rate, and mobility, identified 33 high-risk ARGs. This is essential to evaluate the health risks of ARGs and to develop strategies to limit the threat of antibiotic resistance. Our study offers new insights into the risks associated with ARGs in the environment and suggests that ARGs may depend on specific bacterial cohabitants that co-exist with MGEs to facilitate their spread across environmental interfaces.

Influencing factors on the activity of an enriched Nitrospira culture with granular morphology

Nitrospira is a common genus of nitrite-oxidizing bacteria (NOB) found in wastewater treatment plants (WWTPs). To identify the key factors influencing the composition of NOB communities, research was conducted using both sequencing batch reactor (SBR) and continuous flow reactor under different conditions. High-throughput 16S rRNA gene sequencing revealed that Nitrospira (18.79% in R1 and 25.77% in R3) was the dominant NOB under low dissolved oxygen (DO) and low nitrite (NO2 --N) concentrations, while Nitrobacter (21.26% in R2) was the dominant NOB under high DO and high NO2 --N concentrations. Flocculent and granule sludge were cultivated with Nitrospira as the dominant genus. Compared to Nitrospira flocculent sludge, Nitrospira granule sludge had higher inhibition threshold concentrations for free ammonia (FA) and free nitrous acid (FNA). It was more likely to resist adverse environmental disturbances. Furthermore, the effects of environmental factors such as temperature, pH, and DO on the activity of Nitrospira granular sludge were also studied. The results showed that the optimum temperature and pH for Nitrospira granular sludge were 36 ℃ and 7.0, respectively. Additionally, Nitrospira granular sludge showed a higher dissolved oxygen half-saturation constant (Ko) of 3.67±0.71 mg/L due to its morphological characteristics. However, the majority of WWTPs conditions do not meet the conditions for the Nitrospira granular sludge. Thus, it can be speculated that future development of aerobic partial nitrification granular sludge may automatically eliminate the influence of Nitrospira. This study provides a theoretical basis for a deeper understanding of Nitrospira and the development of future water treatment processes.

Characterization of Lung Microbiomes in Pneumonic Hu Sheep Using Culture Technique and 16S rRNA Gene Sequencing.

Hu sheep, a locally bred species in China known for its high productivity, is currently suffering from pneumonia. Here, we combine high-throughput 16SrRNA gene sequencing and bacterial culturing to examine the bacterial community in pneumonic Hu Sheep lungs (p < 0.05). The results showed that the abundance and diversity of lung bacteria in healthy sheep were significantly higher than those in pneumonia sheep (p = 0.139), while there was no significant difference between moderate and severe pneumonia. Furthermore, the composition of the lung microbiota community underwent significant alterations between different levels of pneumonia severity. The application of LEfSe analysis revealed a notable enrichment of Mannheimiae within the lungs of sheep afflicted with moderate pneumonia (p < 0.01), surpassing the levels observed in their healthy counterparts. Additionally, Fusobacterium emerged as the prevailing bacterial group within the lungs of sheep suffering from severe pneumonia. Integrating the results of bacterial isolation and identification, we conclusively determined that Mannheimia haemolytica was the primary pathogenic bacterium within the lungs of sheep afflicted with moderate pneumonia. Furthermore, the exacerbation of pneumonia may be attributed to the synergistic interplay between Fusobacterium spp. and other bacterial species. Our results provide new insights for guiding preventive and therapeutic measures for pneumonia of different severities in sheep.

Effects of High Dietary Carbohydrate Levels on Growth Performance, Enzyme Activities, Expression of Genes Related to Liver Glucose Metabolism, and the Intestinal Microbiota of Lateolabrax maculatus Juveniles

The present study was conducted to investigate the effects of high dietary carbohydrate levels on growth performance, enzyme activities, and gene expressions related to liver glucose metabolism and the intestinal microbiota of Lateolabrax maculatus juveniles. Two experimental diets with levels of carbohydrates (20% and 30%, named the NCD group and the HCD group, respectively) were designed to feed L. maculatus (initial weight 9.45 ± 0.03 g) for 56 days. The results showed that, compared with the NCD group, the condition factor (CF) was significantly elevated in the HCD group (p &lt; 0.05). The plasma advanced glycosylation end products (AGEs), glycated serum protein (GSP), total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), and glutamate aminotransferase (AST) were significantly higher in the HCD group than those in the NCD group (p &lt; 0.05). The intestinal lipase, chymotrypsin, and α-amylase in the HCD group were significantly higher than those in the NCD group (p &lt; 0.05). The liver superoxide dismutase (SOD), total antioxidant capacity (T-AOC), and catalase (CAT) were significantly lower in the HCD group than in the NCD group (p &lt; 0.05). The liver malondialdehyde (MDA) and hexokinase (HK) levels were significantly higher than those in the NCD group (p &lt; 0.05). In the histopathological findings, liver cells in the HCD group appeared to have many vacuoles, and the number of lipid droplets increased. Compared with the NCD group, the relative expression of liver glucokinase (GK) and glycogen synthetase kinase-3 (GSK3β) genes in the HCD group was significantly increased (p &lt; 0.05), while the relative expression of phosphoenolpyruvate carboxykinase (PEPCK) and glycogen phosphorylase (GP) genes in the HCD group was significantly reduced (p &lt; 0.05). High-throughput 16S rRNA gene sequencing showed that high dietary carbohydrate intake changed the composition and structure of the intestinal microbiota. At the phylum level of the intestinal microbiota, high dietary carbohydrates decreased the relative abundance of Firmicutes and increased the relative abundance of Proteobacteria and Bacteroidetes. At the genus level of the intestinal microbiota, high carbohydrates decreased the relative abundance of Bacillus and increased the relative abundance of Photobacterium and Paraclostridium. From the results of this experiment on L. maculatus, high carbohydrates led to increased condition factor and liver glycogen, lipid deposition, decreased antioxidant capacity of the liver, increased relative abundance of harmful intestinal microorganisms, and disrupted glucose metabolism.

Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota.

Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients.

Fish Gut Microbiome Analysis Provides Insight into Differences in Physiology and Behavior of Invasive Nile Tilapia and Indigenous Fish in a Large Subtropical River in China.

The gut microbiome is thought to play vital roles in host fitness and local adaptation to new environments, thereby facilitating the invasion of the host species. The Nile tilapia (Oreochromis niloticus) (NT) is an aggressive and omnivorous species that competes with native fishes for food resources, and it has successfully invaded much of the Pearl River basin in China. Here, we investigated the gut microbiomes of invasive Nile tilapia and indigenous black Amur bream (BA) in the same river section using high-throughput 16S rRNA gene sequencing. The results indicated that the gut microbiome of NT had several special characteristics, e.g., higher alpha diversity and greater niche breadth, compared with the bream. The gut microbiota of the small size of Nile tilapia (NTS) and small size of black Amur bream (BAS) groups were dominated by Proteobacteria, while those of the NTS and large size of Nile tilapia (NTL) and BAS and large size of black Amur bream (BAL). BAL and NTL were characterized by Firmicutes and Fusobacteriota, respectively. We found that Pseudomonas, Cetobacterium, Ralstonia, and Romboutsia were biomarkers of the NTS, NTL, BAS, and BAL groups, respectively. Moreover, the results collectively suggested that the clustering coefficients of BAL and NTL networks were greater than those of BAS and NTS networks, and BAS had the smallest network among the four groups. Positive interactions between two ASVs dominated the BAS, NTS, and NTL networks, while the proportion of negative interactions between two ASVs in the BAL network was remarkably increased. Low levels of interspecies competition in the NT gut microbiome would contribute to high diversity in the dietary niches and would also benefit the survival and local adaptation of the host. Our results identified specific biomarkers of gut microbial species in invasive Nile tilapia and provided useful information concerning how to monitor and manage invasive Nile tilapia populations.

Exploring Prokaryotic Communities in the Guts and Mucus of Nudibranchs, and Their Similarity to Sediment and Seawater Microbiomes

In the present study, we compared mucus and gut-associated prokaryotic communities from seven nudibranch species with sediment and seawater from Thai coral reefs using high-throughput 16S rRNA gene sequencing. The nudibranch species were identified as Doriprismatica atromarginata (family Chromodorididae), Jorunna funebris (family Discodorididae), Phyllidiella nigra, Phyllidiella pustulosa, Phyllidia carlsonhoffi, Phyllidia elegans, and Phyllidia picta (all family Phyllidiidae). The most abundant bacterial phyla in the dataset were Proteobacteria, Tenericutes, Chloroflexi, Thaumarchaeota, and Cyanobacteria. Mucus and gut-associated communities differed from one another and from sediment and seawater communities. Host phylogeny was, furthermore, a significant predictor of differences in mucus and gut-associated prokaryotic community composition. With respect to higher taxon abundance, the order Rhizobiales (Proteobacteria) was more abundant in Phyllidia species (mucus and gut), whereas the order Mycoplasmatales (Tenericutes) was more abundant in D. atromarginata and J. funebris. Mucus samples were, furthermore, associated with greater abundances of certain phyla including Chloroflexi, Poribacteria, and Gemmatimonadetes, taxa considered to be indicators for high microbial abundance (HMA) sponge species. Overall, our results indicated that nudibranch microbiomes consisted of a number of abundant prokaryotic members with high sequence similarities to organisms previously detected in sponges.

Alteration of gut microbiome and correlated amino acid metabolism are associated with acute myelocytic leukemia carcinogenesis.

The aim of this study is to investigate the profiles of gut microbiota and metabolites in acute myelocytic leukemia (AML) patients treated with/without chemotherapy. Herein, high-throughput 16S rRNA gene sequencing was performed to analysis gut microbiota profiles, and liquid chromatography and mass spectrometry were performed to analysis metabolites profiles. The correlation between gut microbiota biomarkers identified by LEfSe and differentially expressed metabolites were determined by spearman association analysis. The results showed the distinguished gut microbiota and metabolites profiles between AML patients and control individuals or AML patients treated with chemotherapy. Compared to normal populations, the ratio of Firmicutes to Bacteroidetes was increased at the phylum level than that in AML patients, and LEfSe analysis identified Collinsella and Coriobacteriaceae as biomarkers of AML patients. Differential metabolite analysis indicated that, compared to AML patients, numerous differential amino acids and analogs could be observed in control individuals and AML patients treated with chemotherapy. Interestingly, spearman association analysis demonstrated that plenty of bacteria biomarkers shows statistical correlations with differentially expressed amino acid metabolites. In addition, we found that both Collinsella and Coriobacteriaceae demonstrate remarkable positive correlation with hydroxyprolyl-hydroxyproline, prolyl-tyrosine, and tyrosyl-proline. In conclusion, our present study investigated the role of the gut-microbiome-metabolome axis in AML and revealed the possibility of AML treatment by gut-microbiome-metabolome axis in the further.

Tomato Plant Microbiota under Conventional and Organic Fertilization Regimes in a Soilless Culture System.

Tomato is the main vegetable cultivated under soilless culture systems (SCSs); production of organic tomato under SCSs has increased due to consumer demands for healthier and environmentally friendly vegetables. However, organic tomato production under SCSs has been associated with low crop performance and fruit quality defects. These agricultural deficiencies could be linked to alterations in tomato plant microbiota; nonetheless, this issue has not been sufficiently addressed. Thus, the main goal of the present study was to characterize the rhizosphere and phyllosphere of tomato plants cultivated under conventional and organic SCSs. To accomplish this goal, tomato plants grown in commercial greenhouses under conventional or organic SCSs were tested at 8, 26, and 44 weeks after seedling transplantation. Substrate (n = 24), root (n = 24), and fruit (n = 24) composite samples were subjected to DNA extraction and high-throughput 16S rRNA gene sequencing. The present study revealed that the tomato core microbiota was predominantly constituted by Proteobacteria, Actinobacteria, and Firmicutes. Remarkably, six bacterial families, Bacillaceae, Microbacteriaceae, Nocardioidaceae, Pseudomonadaceae, Rhodobacteraceae, and Sphingomonadaceae, were shared among all substrate, rhizosphere, and fruit samples. Importantly, it was shown that plants under organic SCSs undergo a dysbiosis characterized by significant changes in the relative abundance of Bradyrhizobiaceae, Caulobacteraceae, Chitinophagaceae, Enterobacteriaceae, Erythrobacteraceae, Flavobacteriaceae, Nocardioidaceae, Rhodobacteraceae, and Streptomycetaceae. These results suggest that microbial alterations in substrates, roots, and fruits could be potential factors in contributing to the crop performance and fruit quality deficiencies observed in organic SCSs.

Occurrence and Distribution of Tetrabromobisphenol A and Diversity of Microbial Community Structure in the Sediments of Mangrove.

The occurrence and distribution characteristics of tetrabromobisphenol A (TBBPA) and its relationship with microbial community diversity in different mangrove sediments need further investigation. The results of this study indicated levels of TBBPA in mangrove sediments from the Zhangjiang Estuary (ZJ), Jiulongjiang Estuary (JLJ), and Quanzhou Bay (QZ) in Southeast China ranging from 1.80 to 20.46, 3.47 to 40.77, and 2.37 to 19.83 ng/g dry weight (dw), respectively. Mangrove sediments from JLJ contained higher levels of TBBPA, possibly due to agricultural pollution. A correlation analysis revealed a significant correlation between total organic carbon (TOC), total nitrogen (TN), and TBBPA distribution in ZJ and JLJ mangrove sediments, but not in QZ mangrove sediments. TOC significantly affected the distribution of TBBPA in mangrove sediments, but pH had no effect. High-throughput 16S rRNA gene sequencing showed that Pseudomonadota dominated the sediment bacteria followed by Chloroflexota, Actinobacteota, Bacillota, Acidobacteriota, Bacteroidota, and Aminicenantes in mangrove sediments. Although the microbial community structure of the ZJ, JLJ, and QZ mangrove sediments was similar, the taxonomic profile of their sensitive responders differed markedly. The genus Anaerolinea was dominant in the mangrove sediments and was responsible for the in situ dissipation of TBBPA. Based on redundancy analysis, there was a correlation between TBBPA, TOC, TN, C/N, pH, and microbial community structure at the genus level. Combining TBBPA, TN, and TOC may induce variations in the microbial community of mangrove sediments.

Effects of mushroom-tobacco rotation on microbial community structure in continuous cropping tobacco soil.

Rotation is an effective strategy for controlling crop diseases and improving plant health. However, the effect of a mushroom-tobacco rotation on the composition and structure of microbial communities in continuous cropping soil is unclear. This study analysed the structure and function of soil bacterial and fungal communities using Illumina MiSeq high-throughput 16S rRNA gene sequencing. The results showed that the physicochemical properties (organic matter, available nitrogen, available phosphorus, and available potassium) and enzymatic activity (phosphatase, catalase, urease and invertase activity) in the rotation treatments (Y1, M1, Y2 and M2) were significantly higher than those in the control (continuous cropping) treatment (CK) and reached peak values in the M2 treatment. PCA showed that the soil microbial community structure in each rotation treatment was different from that in the control. The dominant bacterial phyla of the different soil treatments were Proteobacteria and Actinobacteriota, and the dominant fungal phyla of the different soil treatments were Ascomycota and Basidiomycota. The M2 rotation significantly reduced the relative abundance of harmful fungi (Penicillium and Gibberella) compared to the other treatments. RDA showed that the most abundant bacterial taxa were negatively correlated with pH and positively correlated with physicochemical properties. However, the most abundant fungal taxa were positively correlated with pH and negatively correlated with physicochemical properties. The mushroom-tobacco rotation can effectively maintain the ecological balance of the substrate microbial environment, and provide a more effective way to prevent the continuous cropping of tobacco.

Effects of biological flocculation technology (BFT) on water quality dynamics and immune response of grass carp (Ctenopharyngodon idella)

The biofloc technology (BFT) offers benefits in improving feed utilization and reducing the feed conversion ratio compared to the recirculating aquaculture system (RAS). In this study, high-throughput 16S rRNA gene sequencing was employed to investigate and compare the bacterial communities in these aquaculture systems and the gut microbiota of grass carp reared in them. We observed a significant distinction between the microbial communities of the aquaculture systems and the intestinal microbiota of grass carp. The genera cetobacterium and bacillus were more abundant in the BFT system, accounting for only 0.05% and 0.25% in the RAS. Our study also demonstrated that BFT could influence the intestinal microorganisms of grass carp (Ctenopharyngodon Idella) by reducing the relative abundance of burkholderia-caballeronia-paraburkholderia and increasing that of cetobacterium. Based on bugBase community predictions, the potential pathogenicity in BFT and grass carp intestine was lower than in RAS. Regarding gene expression in the grass carp intestine, immunosuppressive genes showed higher expression, while pro-inflammatory genes exhibited lower expression in grass carp reared in BFT. Furthermore, the final average length and weight of grass carp in the BFT system were significantly higher than those in the RAS. This study provides valuable insights into gut microbiome ecology in relation to two grass carp aquaculture systems, which could be effectively applied in grass carp management to promote health and improve water quality.

Comparative assessment of the bacterial communities associated with Anopheles darlingi immature stages and their breeding sites in the Brazilian Amazon

BackgroundThe neotropical anopheline mosquito Anopheles darlingi is a major malaria vector in the Americas. Studies on mosquito-associated microbiota have shown that symbiotic bacteria play a major role in host biology. Mosquitoes acquire and transmit microorganisms over their life cycle. Specifically, the microbiota of immature forms is largely acquired from their aquatic environment. Therefore, our study aimed to describe the microbial communities associated with An. darlingi immature forms and their breeding sites in the Coari municipality, Brazilian Amazon.MethodsLarvae, pupae, and breeding water were collected in two different geographical locations. Samples were submitted for DNA extraction and high-throughput 16S rRNA gene sequencing was conducted. Microbial ecology analyses were performed to explore and compare the bacterial profiles of An. darlingi and their aquatic habitats.ResultsWe found lower richness and diversity in An. darlingi microbiota than in water samples, which suggests that larvae are colonized by a subset of the bacterial community present in their breeding sites. Moreover, the bacterial community composition of the immature mosquitoes and their breeding water differed according to their collection sites, i.e., the microbiota associated with An. darlingi reflected that in the aquatic habitats where they developed. The three most abundant bacterial classes across the An. darlingi samples were Betaproteobacteria, Clostridia, and Gammaproteobacteria, while across the water samples they were Gammaproteobacteria, Bacilli, and Alphaproteobacteria.ConclusionsOur findings reinforce the current evidence that the environment strongly shapes the composition and diversity of mosquito microbiota. A better understanding of mosquito–microbe interactions will contribute to identifying microbial candidates impacting host fitness and disease transmission.Graphical

Intravenous antibiotics in preterm infants have a negative effect upon microbiome development throughout preterm life

BackgroundIntestinal dysbiosis is implicated in the origins of necrotising enterocolitis and late-onset sepsis in preterm babies. However, the effect of modulators of bacterial growth (e.g. antibiotics) upon the developing microbiome is not well-characterised.In this prospectively-recruited, retrospectively-classified, case–control study, high-throughput 16S rRNA gene sequencing was combined with contemporaneous clinical data collection, to assess the within-subject relationship between antibiotic administration and microbiome development, in comparison to preterm infants with minimal antibiotic exposure.ResultsDuring courses of antibiotics, diversity progression fell in comparison to that seen outside periods of antibiotic use (-0.71units/week vs. + 0.63units/week, p < 0.01); Enterobacteriaceae relative abundance progression conversely rose (+ 10.6%/week vs. -8.9%/week, p < 0.01). After antibiotic cessation, diversity progression remained suppressed (+ 0.2units/week, p = 0.02).ConclusionsAntibiotic use has an acute and longer-lasting impact on the developing preterm intestinal microbiome. This has clinical implications with regard to the contribution of antibiotic use to evolving dysbiosis, and affects the interpretation of existing microbiome studies where this effect modulator is rarely accounted for.

Potential of indigenous bacteria driven U(VI) reduction under relevant deep geological repository (DGR) conditions

Understanding the biogeochemical U redox processes is crucial for controlling U mobility and toxicity under conditions relevant to deep geological repositories (DGRs). In this study, we examined the microbial reduction of aqueous hexavalent uranium U(VI) [U(VI)aq] by indigenous bacteria in U-contaminated groundwater. Three indigenous bacteria obtained from granitic groundwater at depths of 44–60 m (S1), 92–116 m (S2), and 234–244 m (S3) were used in U(VI)aq bioreduction experiments. The concentration of U(VI)aq was monitored to evaluate its removal efficiency for 24 weeks under anaerobic conditions with the addition of 20 mM sodium acetate. During the anaerobic reaction, U(VI)aq was precipitated in the form of U(IV)-silicate with a particle size >100 nm. The final U(VI)aq removal efficiencies were 37.7%, 43.1%, and 57.8% in S1, S2, and S3 sample, respectively. Incomplete U(VI)aq removal was attributed to the presence of a thermodynamically stable calcium uranyl carbonate complex in the U-contaminated groundwater. High-throughput 16S rRNA gene sequencing analysis revealed the differences in indigenous bacterial communities in response to the depth, which affected to the U(VI)aq removal efficiency. Pseudomonas peli was found to be a common bacterium related to U(VI)aq bioreduction in S1 and S2 samples, while two SRB species, Thermodesulfovibrio yellowstonii and Desulfatirhabdium butyrativorans, played key roles in the bioreduction of U(VI)aq in S3 sample. These results indicate that remediation of U(VI)aq is possible by stimulating the activity of indigenous bacteria in the DGR environment.

Carapace microbiota in American lobsters (Homarus americanus) associated with epizootic shell disease and the green gland.

Epizootic Shell Disease (ESD) has posed a great threat, both ecologically and economically, to the American lobster population of Long Island Sound since its emergence in the late 1990s. Because of the polymicrobial nature of carapace infections, causative agents for ESD remain unclear. In this study, we aimed to identify carapace microbiota associated with ESD and its potential impact on the microbiota of internal organs (green gland, hepatopancreas, intestine, and testis) using high-throughput 16S rRNA gene sequencing. We found that lobsters with ESD harbored specific carapace microbiota characterized by high abundance of Aquimarina, which was significantly different from healthy lobsters. PICRUSt analysis showed that metabolic pathways such as amino acid metabolism were enriched in the carapace microbiota of lobsters with ESD. Aquimarina, Halocynthiibacter, and Tenacibaculum were identified as core carapace bacteria associated with ESD. Particularly, Aquimarina and Halocynthiibacter were detected in the green gland, hepatopancreas, and testis of lobsters with ESD, but were absent from all internal organs tested in healthy lobsters. Hierarchical clustering analysis revealed that the carapace microbiota of lobsters with ESD was closely related to the green gland microbiota, whereas the carapace microbiota of healthy lobsters was more similar to the testis microbiota. Taken together, our findings suggest that ESD is associated with alterations in the structure and function of carapace microbiota, which may facilitate the invasion of bacteria into the green gland.

Mulberry leaf water extract alleviates type 2 diabetes in mice via modulating gut microbiota-host co-metabolism of branched-chain amino acid.

Elevations in circling branched-chain amino acids (BCAAs) levels associated with insulin resistance and type 2 diabetes mellitus (T2DM). Morus alba L. water extracts (MLE) show hypoglycemic function, but the precise mechanism remains obscure. This study is designed to investigate the association of the antidiabetes effect of MLE with the BCAAs co-metabolism modulated by host and gut microbiota. Tissue-specific expressions of BCAA-catabolizing enzymes were detected by RT-PCR and western blot, respectively. The components of the intestinal microflora were analyzed by high-throughput 16S rRNA gene sequencing. The results showed that MLE administration improved blood glucose and insulin level, decreased inflammatory cytokines expression, and lowered serum and feces BCAAs levels. Furthermore, MLE reversed the abundance changes of the bacterial genera correlated with serum and feces BCAAs, such as Anaerovorax, Bilophila, Blautia, Colidextribacter, Dubosiella, Intestinimonas, Lachnoclostridium, Lachnospiraceae_NK4A136, Oscillibacter, and Roseburia. Functionality prediction indicated that MLE potentially inhibited bacterial BCAAs biosynthesis, and promoted the tissue-specific expression of BCAAs catabolic enzyme. More importantly, MLE had obvious impacts on BCAA catabolism in germ-free-mimic T2DM mice. Those results indicated that MLE improving T2DM-related biochemical abnormalities is associated with not only gut microbiota modification but also the tissue-specific expression of BCAAs catabolic enzyme.

Assessing the Relationship Between Gut Microbiota and Posttransplant Diabetes Mellitus.

The incidence of diabetes significantly increases after kidney transplant, and the associated gut microbiota are closely related to diabetes. However, the gut microbiota of recipients with diabetes after kidney transplant remain unexplored. Feces samples from recipients with diabetes 3 months after kidney transplant were collected and analyzed using high-throughput 16S rRNA gene sequencing. Our study included 45 transplant recipients: 23 posttransplant diabetes mellitus recipients, 11 recipients without diabetes mellitus, and 11 recipients with preexisting diabetes mellitus. No significant differences in intestinal flora richness and α diversity were observed among the 3 groups. However, principal coordinate analysis based on UniFrac distance revealed significant differences in β diversity. At the phyla level, the abundance of Proteobacteria in posttransplant diabetes mellitus recipients decreased (P = .028), whereas that of Bactericide (P = .004) increased. At the class level, the abundance of Gammaproteobacteria (P = .037) decreased, whereas thatofBacteroidia (P=.004)increased.Attheorderlevel, the abundanceof Enterobacteriales (P = .039)decreased, whereasBacteroidales (P=.004)increased.Atthe family level, the abundance of Enterobacteriaceae (P = .039) and Peptostreptococcaceae (P = .008) decreased, whereas Bacteroidaceae (P = .010) increased. At the genus level,the abundance of Lachnospiraceae incertae sedis (P = .008) decreased, whereas Bacteroides (P = .010) increased. Furthermore, KEGG analysis identified 33 pathways, among which the biosynthesis of unsaturated fatty acids was closely related to gut microbiota and posttransplant diabetes mellitus. To our knowledge, this is the first comprehensive analysis of the gut microbiota from posttransplant diabetes mellitus recipients. The microbial composition of stool samples of post- transplant diabetes mellitus recipients was significantly different from recipients without diabetes and with preexisting diabetes. The number of bacteria producing short-chain fatty acids decreased, whereas pathogenic bacteria increased.

Distinct community assembly processes and habitat specialization driving the biogeographic patterns of abundant and rare bacterioplankton in a brackish coastal lagoon

The ecological diversity patterns and community assembly processes along spatio-temporal scales are least studied in the bacterioplankton sub-communities of brackish coastal lagoons. We examined the biogeographic patterns and relative influences of different assembly processes in structuring the abundant and rare bacterioplankton sub-communities of Chilika, the largest brackish water coastal lagoon of India. Rare taxa demonstrated significantly higher α- and β-diversity and biogeochemical functions than abundant taxa in the high-throughput 16S rRNA gene sequence dataset. The majority of the abundant taxa (91.4 %) were habitat generalists with a wider niche breadth (niche breadth index, B = 11.5), whereas most of the rare taxa (95.2 %) were habitat specialists with a narrow niche breadth (B = 8.9). Abundant taxa exhibited a stronger distance-decay relationship and higher spatial turnover rate than rare taxa. β-diversity partitioning revealed that the contribution of species turnover (72.2–97.8 %) was greater than nestedness (2.2–27.8 %) in causing the spatial variation in both abundant and rare taxa. Null model analyses revealed that the distribution of abundant taxa was mostly structured by stochastic processes (62.8 %), whereas deterministic processes (54.1 %) played a greater role in the rare taxa. However, the balance of these two processes varied across spatio-temporal scales in the lagoon. Salinity was the key deterministic factor controlling the variation of both abundant and rare taxa. Potential interaction networks showed a higher influence of negative interactions, indicating that species exclusion and top-down processes played a greater role in the community assembly. Notably, abundant taxa emerged as keystone taxa across spatio-temporal scales, suggesting their greater influences on other bacterial co-occurrences and network stability. Overall, this study provided detailed mechanistic insights into biogeographic patterns and underlying community assembly processes of the abundant and rare bacterioplankton over spatio-temporal scales in a brackish lagoon.

Brassica rapa subsp. Chinensis juice enhances Bacillus subtilis selectively in leafy green production.

Bacillus subtilis (BS) is a well-known beneficial microorganism for plants but is not competitive in the plant rhizosphere microbiome. We report the selective support of Brassica rapa subsp. Chinensis (Xiao Bai Cai) juice (XBCJ) on BS both in hydroponic nutrient solution and the plant rhizosphere of lettuce. After 2 weeks of being inoculated in the lettuce rhizosphere, the Bacillus population was enumerated at 3.30 ± 0.07 log CFU/unit in the BS group and at 5.20 ± 0.39 log CFU/unit in the BS + XBCJ group (p< 0.05). Accordingly, lettuce crops from the BS + XBCJ group were significantly higher than the control group for all of the tested biomass-related parameters (p< 0.05). The treatment did not significantly affect the texture, colour, moisture contents, total phenolic contents, or antioxidant activities of the lettuce crops (p> 0.05). Non-target ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) suggested that phenolic compounds could be the key class of phytochemicals being responsible for the selectivity. High-throughput RNA-based 16S rRNA gene sequencing and analysis were performed to depict the influence of BS and XBCJ over the global microbiome compositions of plant rhizosphere.