Preliminary study on mitochondrial 16S rRNA gene sequences and phylogeny of flatfishes (Pleuronectiformes)

A 605 bp section of mitochondrial 16S rRNA gene from Paralichthys olivaceus, Pseudorhombus cinnamomeus, Psetta maxima and Kareius bicoloratus, which represent 3 families of Order Pleuronectiformes was amplified by PCR and sequenced to show the molecular systematics of Pleuronectiformes for comparison with related gene sequences of other 6 flatfish downloaded from GenBank. Phylogenetic analysis based on ge- netic distance from related gene sequences of 10 flatfish showed that this method was ideal to explore the rela- tionship between species, genera and families. Phylogenetic trees set-up is based on neighbor-joining, maximum parsimony and maximum likelihood methods that accords to the general rule of Pleuronectiformes evolution. But they also resulted in some confusion. Unlike data from morphological characters, P. olivaceus clustered with K. bicoloratus, but P. cinnamomeus did not cluster with P. olivaceus, which is worth further studying.

Causal Relationship Between Gut Microbiota and Liver Cirrhosis:16S rRNA Sequencing and Mendelian Randomization Analyses

Background and Aims:Accumulating evidence highlights the association between the gut microbiota and liver cirrhosis.However,the role of the gut microbiota in liver cirrhosis remains unclear.Methods:We first assessed the differences in the composition of the bacterial community between CCl4-induced liver cirrhosis and control mice using 16S rRNA sequencing.We then performed a two-sample Mendelian randomization(MR)analysis to reveal the underlying causal relationship between the gut microbiota and liver cirrhosis.Causal relationships were analyzed using primary inverse variance weighting(IVW)and other supplemental MR methods.Furthermore,fecal samples from liver cirrhosis patients and healthy controls were collected to validate the results of the MR analysis.Results:Analysis of 16S rRNA sequencing indicated significant differences in gut microbiota composition between the cirrhosis and control groups.IVW analyses suggested that Alphaproteobacteria,Bacillales,NB1n,Rhodospirillales,Dorea,Lachnospiraceae,and Rhodospirillaceae were positively correlated with the risk of liver cirrhosis,whereas Butyricicoccus,Hungatella,Marvinbryantia,and Lactobacillaceae displayed the opposite effects.However,the weighted median and MR-PRESSO estimates further showed that only Butyricicoccus and Marvinbryantia presented stable negative associations with liver cirrhosis.No significant heterogeneity or horizontal pleiotropy was observed in the sensitivity analysis.Furthermore,the result of 16S rRNA sequencing also showed that healthy controls had a higher relative abundance of Butyricicoccus and Marvinbryantia than liver cirrhosis patients.Conclusions:Our study provides new causal evidence for the link between gut microbiota and liver cirrhosis,which may contribute to the discovery of novel strategies to prevent liver cirrhosis.

Sarcopenia and gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation

Objective: The aim of this study was to investigate the prevalence of sarcopenia(SP) and its relationship with gut microbiota alterations in patients with hematological diseases before and after hematopoietic stem cell transplantation(HSCT).Methods: A total of 108 patients with various hematological disorders were selected from Peking University People’s Hospital. SP was screened and diagnosed based on the 2019 Asian Sarcopenia Diagnosis Strategy. Physical measurements and fecal samples were collected, and 16S rRNA gene sequencing was conducted. Alpha and beta diversity analyses were performed to evaluate gut microbiota composition and diversity.Results: After HSCT, significant decreases in calf circumference and body mass index(BMI) were observed,accompanied by a decline in physical function. Gut microbiota analyses revealed significant differences in the relative abundance of Enterococcus, Bacteroides, Blautia and Dorea species before and after HSCT(P<0.05). Before HSCT, sarcopenic patients had lower Dorea levels and higher Phascolarctobacterium levels than non-sarcopenia patients(P<0.01). After HSCT, no significant differences in species abundance were observed. Alpha diversity analysis showed significant differences in species diversity among the groups, with the highest diversity in the postHSCT 90-day group and the lowest in the post-HSCT 30-day group. Beta diversity analysis revealed significant differences in species composition between pre-and post-HSCT time points but not between SP groups. Linear discriminant analysis effect size(LEfSe) identified Alistipes, Rikenellaceae, Alistipes putredinis, Prevotellaceae defectiva and Blautia coccoides as biomarkers for the pre-HSCT sarcopenia group. Functional predictions showed significant differences in anaerobic, biofilm-forming and oxidative stress-tolerant functions among the groups(P<0.05).Conclusions: This study demonstrated a significant decline in physical function after HSCT and identified potential gut microbiota biomarkers and functional alterations associated with SP in patients with hematological disorders. Further research is needed to explore the underlying mechanisms and potential therapeutic targets.

Alterations in gut microbiota are related to metabolite profiles in spinal cord injury

Studies have shown that gut microbiota metabolites can enter the central nervous system via the blood-spinal cord barrier and cause neuroinflammation, thus constituting secondary injury after spinal cord injury. To investigate the correlation between gut microbiota and metabolites and the possible mechanism underlying the effects of gut microbiota on secondary injury after spinal cord injury, in this study, we established mouse models of T8–T10 traumatic spinal cord injury. We used 16 S rRNA gene amplicon sequencing and metabolomics to reveal the changes in gut microbiota and metabolites in fecal samples from the mouse model. Results showed a severe gut microbiota disturbance after spinal cord injury, which included marked increases in pro-inflammatory bacteria, such as Shigella, Bacteroides, Rikenella, Staphylococcus, and Mucispirillum and decreases in anti-inflammatory bacteria, such as Lactobacillus, Allobaculum, and Sutterella. Meanwhile, we identified 27 metabolites that decreased and 320 metabolites that increased in the injured spinal cord. Combined with pathway enrichment analysis, five markedly differential amino acids(L-leucine, L-methionine, L-phenylalanine, L-isoleucine and L-valine) were screened out, which play a pivotal role in activating oxidative stress and inflammatory responses following spinal cord injury. Integrated correlation analysis indicated that the alteration of gut microbiota was related to the differences in amino acids, which suggests that disturbances in gut microbiota might participate in the secondary injury through the accumulation of partial metabolites that activate oxidative stress and inflammatory responses. Findings from this study provide a new theoretical basis for improving the secondary injury after spinal cord injury through fecal microbial transplantation.

Spatiotemporal dynamics of the microbial diversity on salt-preserved goatskins assessed by culturing and 16S rRNA gene amplicon sequencing

Wet-salted skin,as a special artificial high-salt environment,is rich in protein,fat,collagen and other nutrient substrates,and is a rich resource of halotolerant and halophilic microorganisms.However,knowledge gaps regarding the microbial community structure and inter taxa associations of wet-salted skin are large.In this study,the spatiotemporal dynamics and community structure of microorganisms present on wet-salted goatskins were investigated using 16S rRNA gene amplicon sequencing and culturable technique.Alpha diversity analysis based on Sobs,Chao,Ace and Shannon indices revealed that microbial diversity on the wet-salted goatskins exhibited a trend of‘down→up→down→flat’with time.During preservation,genera belonging to the bacteria domain such as Aci-netobacter,Weissella and Streptococcus were slowly dying out,whereas those belonging to halophilic archaea such as Natrialba and Haloterrigena were gradually flourishing.Moreover,to resist high-salt stress,microorganisms on the wet-salted goatskin gradually migrated from the outside to the inside,eventually leading to the microbial diversity inside the skin being the same as or even higher than that on the skin surface.Venn diagram analysis revealed that the strains of some genera,including Psychrobacter,Salimicrobium,Salinicola,Ornithinibacillus,Halomonas,Bacillus and Chromohalobacter,were distributed throughout the interior and exterior of the wet-salted goatskin and existed during various periods.Accordingly,45 protease-producing halophilic or halotolerant microorganisms were isolated and screened from the wet-salted goatskin using the gradient dilution plate method.Importantly,16S rRNA genes of some bacteria exhibited less than 99.5%similarity to valid published species,indicating that they likely are novel spe-cies and have a good potential for application.

Effects of sepsis and its treatment measures on intestinal flora structure in critical care patients

BACKGROUND Sepsis is a common disease in intensive care units,with high morbidity and mortality.Intestinal microecology plays a vital part in the development and progression of this disease,possibly because sepsis and its treatment cause specific changes in the composition of the intestinal flora.AIM To investigate the characteristics of intestinal flora disturbance in sepsis patients treated with antibiotics.METHODS In this prospective comparative study,we enrolled ten patients with sepsis(sepsis group),hospitalized in the Department of Critical Care Medicine of the General Hospital,Ningxia Medical University,China(a class IIIa general hospital)from February 2017 to June 2017;ten patients without sepsis hospitalized in the same period(non-sepsis group)and ten healthy individuals(control group)were also enrolled.Fecal samples collected from the three groups were subjected to 16S rRNA gene sequencing and the intestinal flora diversity,structure,and composition were determined.Additionally,the dynamics of the intestinal flora diversity,structure,and composition in sepsis patients were investigated via 16S rRNA gene sequencing of samples collected 0 d,3 d,and 7 d after admittance to the intensive care unit.Correlations between the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid and the intestinal flora composition of sepsis patients were also investigated.RESULTS Compared with the healthy control group,sepsis and non-sepsis patients showed reduced intestinal floraα-diversity and a distinct flora structure,with Firmicutes as the dominant phylum,and significantly decreased proportions of Bacteroidetes,as well as Prevotella and Lachnospira,among other genera.Of note,the proportion of Enterococcus was significantly increased in the intestinal tract of sepsis patients.Interestingly,theα-diversity in the sepsis group decreased gradually,from days 1 to 7 of treatment.However,pairwise comparisons showed that both the diversity and structure of the intestinal flora were not significantly different considering the three different time points studied.Curiously,the serum levels of procalcitonin,endotoxin,diamine oxidase,and D-lactic acid in sepsis patients correlated with the prevalence of various bacterial genera.For example,the prevalence of Ruminococcus was positively correlated with serum procalcitonin,endotoxins,and diamine oxidase;similarly,the prevalence of Roseburia was positively correlated with serum procalcitonin,endotoxins,and D-lactic acid.CONCLUSION Sepsis patients in intensive care units show dysbiosis,lasting for at least 1 wk.

Disruption of bacterial balance in the gut of Portunus trituberculatus induced by Vibrio alginolyticus infection

A bstract Gut microbiota impacts the health of crustaceans. V ibrio alginolyticus is a main causative pathogen that induces the vibriosis in farmed swimming crabs, Portunus trituberculatus. However, it remains unknown whether gut bacteria perform functions during the progression of vibriosis. In this study, 16 SrRNA gene amplicon sequencing was used to investigate temporal alteration of gut bacterial community in swimming crabs in response to 72-h V. alginolyticus challenge. Our results show that V. alginolyticus infection resulted in dynamic changes of bacterial community composition in swimming crabs. Such changes were highlighted by the overwhelming overabundance of V ibrio and a significant fluctuation in the gut bacteria including the bacteria with high relative abundance and especially those with low relative abundance. These findings reveal that crab vibriosis gradually develops with the infection time of V. alginolyticus and tightly relates to the dysbiosis of gut bacterial community structure. This work contributes to our appreciation of the importance of the balance of gut bacterial community structure in maintaining the health of crustaceans.

A novel apidaecin Api-PR19 synergizes with the gut microbial community to maintain intestinal health and promote growth performance of broilers

Background: Antibiotic growth promoters(AGPs) have been used as growth promoters to maintain animal intestinal health and improve feed efficiency in broilers by inhibiting pathogen proliferation. In view of the growing emergence of antibiotic-resistant pathogen strains and drug residue issues, novel treatments are increasingly required. This study aimed to compare two antimicrobial approaches for managing pathogen infection and maintaining animal intestinal health in broilers by supplying Apidaecin Api-PR19 and AGPs over 42 d of a feeding trial.Results: Compared with the broilers that were only fed a corn-soybean basal diet(CON group), supplementation with Api-PR19 and AGP(respectively named the ABP and AGP groups) both increased the feed conversion efficiency. When compared with the AGP group, Api-PR19 supplementation could significantly increase the organ index of the bursa of fabricius and subtype H9 antibody level in broiler chickens. Moreover, when compared with the CON group, the intestinal villus height, intestinal nutrient transport, and intestinal s Ig A content were all increased in the Api-PR19 group, while AGP supplementation was harmful to the intestinal villus height and intestinal nutrient transport. By assessing the antibacterial effect of Api-PR19 and antibiotics in vitro and in vivo, we found that Api-PR19 and antibiotics both inhibited the growth of pathogens, including Escherichia coli and Campylobacter jejuni. Furthermore, by using 16 S r RNA gene sequencing, the beneficial bacteria and microbiota in broilers were not disturbed but improved by apidaecin Api-PR19, including the genera of Eubacterium and Christensenella and the species of uncultured_Eubacterium_sp, Clostridium_asparagiforme, and uncultured_Christensenella_sp, which were positively related to improved intestinal development, absorption, and immune function.Conclusion: Apidaecin Api-PR19 treatment could combat pathogen infection and had little negative impact on beneficial bacteria in the gut compared to antibiotic treatment, subsequently improving intestinal development,absorption, and immune function.

Influence of group B streptococcus and vaginal cleanliness on the vaginal microbiome of pregnant women

BACKGROUND The vaginal microbiome plays a critical role in the health of pregnant women and their newborns.Group B Streptococcus(GBS)and vaginal cleanliness significantly affect the vaginal microecosystem and are closely associated with vaginal diseases.AIM To explore the effects of GBS status and vaginal cleanliness on vaginal microecosystems.METHODS We collected 160 vaginal swabs from pregnant women and divided them into the following four groups based on GBS status and vaginal cleanliness:GBS-positive+vaginal cleanliness I–II degree,GBS-negative+vaginal cleanliness I–II degree,GBS-positive+vaginal cleanliness III–IV degree,and GBS-negative+vaginal cleanliness III–IV degree.Samples were subjected to 16S rRNA gene amplicon sequencing.RESULTS Alpha diversity analysis showed that the Shannon index did not significantly differ between the four groups.We identified significant variation in taxa abundance between the GBS-positive and GBS-negative groups and between the vaginal cleanliness I–II degree and III–IV degree groups.Principal coordinate analysis and non-metric multidimensional scaling analysis further confirmed the microbial diversity of the four groups.Moreover,the linear discriminant analysis demonstrated that Lactobacillus jensenii and Actinobacteria were strongly associated with GBS-positive status,and Lactobacillus iners,Lactobacillaceae,Lactobacillus,Lactobacillales,Bacilli and Firmicutes were closely correlated with GBS-negative status.CONCLUSION GBS status and vaginal cleanliness significantly affect vaginal microbiome differences in pregnant women.Our findings provide instructional information for clinical antibiotic treatment in pregnant women with different GBS statuses and vaginal cleanliness degrees.

Metagenomic approach revealed effects of forest thinning on bacterial communities in the forest soil of Mt. Janggunbong, South Korea

The soil microbiome that plays important ecological roles in mountains and forests is influenced by anthropogenic and natural causes.Human activity,particularly harvesting or thinning,affects the soil microbiome in forests by altering environmental conditions,such as vegetation,microclimate,and soil physicochemical properties.The purpose of this study was to investigate the effects on forest thinning on the diversity and composition of the soil bacterial community.From next-generation sequencing results of the 16S rRNA gene,we examined differences in soil bacterial diversity and community composition before and after thinning at Mt.Janggunbong,South Korea.We identified 40 phyla,103 classes,192 orders,412families,947 genera,and 3,145 species from the soil samples.Acidobacteria and Proteobacteria were the most dominant bacterial phyla in the forest soil of Mt.Janggunbong.Soil bacterial diversity measures(richness,Shannon diversity index,and evenness)at the phylum level increased after thinning,whereas species-level taxonomic richness decreased after thinning.Thinning provided new opportunities for bacterial species in Chloroflexi,Verrucomicrobia,Nitrospirae,and other nondominant bacterial taxa,especially for those not found in Mt.Janggunbong before thinning,to settle and adapt to the changing environment.Our results suggested that thinning affected the diversity and composition of soil bacterial communities in forests and mountains.

Prevalence of Bacillus sp.among the biofilm forming community on Ti surface in marine environment

Prevalence of bacterial species involved in biomineralization of manganese on titanium （Ti） surfaces in marine environment was revealed in this research work. This study involves one year sea water exposure of Ti and their periodical biofilm characterization was carried out to quantify the manganese oxidizing bacterial （MOB） presence in the biofilm formed on titanium surfaces. The total viable count study of Ti coupons exposed to sea water for one year resulted in 60% of the MOB in overall biofilm population. The biochemical characterization of MOB isolates were performed for the genus level identifcation of the seven bacterial isolates. Further, the seven strains were subjected to 16S rRNA gene sequencing. Evolutionary analysis was performed using MEGA 7 to obtain closely related strains within the groups. The manganese oxidizing ability of the bacterial isolates were determined with Leucoberbelin Blue Assay （LBB） and Atomic Absorption Spectroscopy studies （hAS）. The results show that among the isolated marine MOB species, Bacillus sp. and Leptothrix sp. have the maximum Mn oxidizing property. The microtitre plate assay was performed to determine the biofilm forming ability of the isolated marine MOB species. All the results have confirmed the prevalence of Bacillus sp. among the biofilm colonizers on Ti surfaces when exposed in sea water.

Effect of gastrointestinal heat retention syndrome on gut microbiota in children with upper respiratory tract infection and lung-heat syndrome

Objective:Gastrointestinal heat retention syndrome(GHRS)is associated with lung-heat syndrome and is related to recurrent respiratory infection.Upper respiratory tract infection(URTI)lung heat syndrome is common in children.The study will explore the effect of GHRS on the structure and function of gut microbiota in children with URTI lung-heat syndrome.Methods:Participants were divided into both groups using the self-developed URTI scale and the“GHRS Diagnostic Scale$Pediatric Part”:GHRS-positive children(LS group)and GHRS-negative children(L group).General information,clinical symptoms,and stool were collected.We used 16S rRNA amplicon sequencing technology to determine the gene sequence of the V3eV4 region in feces and measure the gut microbiota of the both groups at the genus level.Results:A total of 23 children were included in the both groups.There were 12 cases in the LS group and 11 cases in the L group.There was no statistical difference between the both groups in age,gender,height,weight,and body mass index.The effective sequences shared by the both groups accounted for 85.66%of the total.In the gut microbiota,there was no difference in the a diversity and the b diversity between the both groups.Compared with the L group,the LS group had a significant increase in the relative abundance of the Ruminococcus gnavus group,Prevotella-9,Staphylococcus,and Actinomyces(P<.05).The functions of the both groups of microbiota primarily concentrate on metabolism,genetic information processing,and environmental information processing.The relative abundance of signaling molecules and interactions in the LS group were higher than that in the L group(P<.05).The redundancy analysis(RDA)showed that the URTI score had the greatest impact on the distribution of microbiota.Conclusion:GHRS may affect the development of URTI lung-heat syndrome by changing the relative abundances of gut microbiota.

Correlation analysis of intestinal flora and pathological process of type 2 diabetes mellitus

Objective: To observe the relationship between the different stages of type 2 diabetes mellitus(T2DM)and the intestinal flora and verify its underlying mechanism.Methods: T2DM rats were generated by high-fat diet(HFD) combined with intraperitoneal streptozotocin(STZ) injection. The rats were divided into four groups: the control group(fed with normal feed for1 month), the HFD group(fed with HFD for 1 month), the T2DM group(HFD combined with STZ and blood glucose ≥11.1 m M), and the unformed T2DM model(Un-mod) group(HFD combined with STZ and blood glucose <11.1 m M). Feces were collected, and bacterial communities in the fecal samples were analyzed by 16S r RNA gene sequencing. The content of short-chain fatty acids(SCFAs) in feces was measured by gas chromatography. Western blot and quantitative real-time polymerase chain reaction were used to detect the expression of G protein-coupled receptor 41(GPR41) and GPR43.Results: At different stages of T2DM, the intestinal flora and SCFAs content of rats were significantly decreased(all P <.05). Our results indicated that g__Prevotella had a significant negative correlation, and g__Ruminococcus_torques_group and g__lachnoclastic had a significant positive correlation with blood glucose. The content of SCFAs, in particular acetate and butyrate, in rat feces of different stages of T2DM were significantly reduced, as well as GPR41 and GPR43 expression. The results in the Un-mod group were similar to the T2DM group, and the expression of GPR41 and GPR43 proteins were significantly higher than those in the T2DM group(both P <.001).Conclusion: The intestinal flora-SCFAs-GPR41/GPR43 network may be important in the development of T2DM. Decreasing blood glucose levels by regulating the intestinal flora may become a new therapeutic strategy for T2DM, which has very important clinical and social values.

First case of biliary Aureimonas altamirensis infection in a patient with colon cancer in China

Aureimonas altamirensis,first reported in 2006,is an aerobic,gram-negative bacillus.It is usually considered a contaminant from the surrounding environment;however,recent evidences suggest that it may be an opportunistic pathogen in humans,which may cause multiple-site infections.Here,we report the first case of biliary A.altamirensis infection in a patient with colon cancer in Guangzhou,China.The A.altamirensis strain GZ8HT01 was isolated from the bile culture taken from the patient and identified by 16S ribosomal RNA gene sequencing.Additionally,the bacterial strain was sensitive to all antibiotics tested.The patient was effectively treated with imipenem-cilastatin.These findings are valuable for the early diagnosis and effective treatment of this emerging pathogen.

Integrated'omics analysis for the gut microbiota response to moxibustion in a rat model of chronic fatigue syndrome

OBJECTIVE:To observe the efficacy of moxibustion in the treatment of chronic fatigue syndrome(CFS)and explore the effects on gut microbiota and metabolic profiles.METHODS:Forty-eight male Sprague-Dawley rats were randomly assigned to control group(Con),CFS model group(Mod,established by multiple chronic stress for 35 d),MoxA group(CFS model with moxibustion Shenque(CV8)and Guanyuan(CV4),10 min/d,28 d)and MoxB group(CFS model with moxibustion Zusanli(ST36),10 min/d,28 d).Open-field test(OFT)and Morris-water-maze test(MWMT)were determined for assessment the CFS model and the therapeutic effects of moxibustion.16S rRNA gene sequencing analysis based gut microbiota integrated untargeted liquid chromatograph-mass spectrometer(LC-MS)based fecal metabolomics were executed,as well as Spearman correlation analysis,was utilized to uncover the functional relevance between the potential metabolites and gut microbiota.RESULTS:The results of our behavioral tests showed that moxibustion improved the performance of CFS rats in the OFT and the MWMT.Microbiome profiling analysis revealed that the gut microbiomes of CFS rats were less diverse with altered composition,including increases in pro-inflammatory species(such as Proteobacteria)and decreases in anti-inflammatory species(such as Bacteroides,Lactobacillus,Ruminococcus,and Prevotella).Moxibustion partially normalized these changes in the gut microbiota.Furthermore,CFS was associated with metabolic disorders,which were effectively ameliorated by moxibustion.This was demonstrated by the normalization of 33 microbiota-related metabolites,including mannose(P=0.001),aspartic acid(P=0.009),alanine(P=0.007),serine(P=0.000),threonine(P=0.027),methionine(P=0.023),5-hydroxytryptamine(P=0.008),alpha-linolenic acid(P=0.003),eicosapentaenoic acid(P=0.006),hypoxanthine(P=0.000),vitamin B6(P=0.000),cholic acid(P=0.013),and taurocholate(P=0.002).Correlation analysis showed a significant association between the perturbed fecal microbiota and metabolite levels,with a notable negative relationship between LCA and Bacteroides.CONCLUSIONS:In this study,we demonstrated that moxibustion has an antifatigue-like effect.The results from the 16S rRNA gene sequencing and metabolomics analysis suggest that the therapeutic effects of moxibustion on CFS are related to the regulation of gut microorganisms and their metabolites.The increase in Bacteroides and decrease in LCA may be key targets for the moxibustion treatment of CFS.

Catalog of operational taxonomic units and unified amplicon sequencing data for the microbiomes of medicinal plant roots

China has a rich history of cultivating medicinal plants,whose root microbial communities closely interact with the medicinal plants,thereby influencing their growth,health,and medicinal properties.Currently,researchers widely use 16S rRNA gene amplicon sequencing to study these root microbial communities.However,publicly available sequence datasets often lack essential sample information or contain errors,impeding the reuse of the datasets in the future.In this study,we aimed to create a united,reliable,and readily usable source of 16S rRNA gene sequences for medicinal plant root microbiomes.We compiled a catalog of 1392 microbiome samples for 58 medicinal plants from 58 studies,and manually provided essential sample information based on the experimental setup described in the associated papers.We then processed the sequences using a custom pipeline,generating a united catalog of operational taxonomic units(OTUs)and conducting taxonomic classification.We also pre-dicted the ecological functions of the communities for each sample.Finally,we used this dataset,to compare the rhizosphere bacterial communities of Pseudostellaria heterophylla from Fujian and Guizhou Provinces,revealing significant differences in the community composition of the same plant from different geographic locations.By providing a comprehensive and united catalog of amplicon sequences and OTUs for medicinal plant root bacterial communities,this study offers an invaluable resource for future comparative studies and data mining.

Soil properties and habitats determine the response of bacterial communities to agricultural wastewater irrigation

Increasing temperatures and variability of precipitation events due to climate change will lead in the future to higher irrigation demands in agroecosystems.However,the use of secondary treated wasterwater(TWW)could have consequences for the receiving soil environment and its resident microbial communities.The objective of this study was to characterize the importance of soil properties and habitats to the response of soil bacteria and archaea to irrigation with TWW.Two agricultural soils with contrasting textures(loamy sand or silt loam)and,for each,three variants differing in soil organic carbon and nitrogen,as generated by long-term fertilization,were analyzed.For each of these six soils,prokaryotic communities from two habitats,i.e.,root-free bulk soil and the rhizosphere of developing cucumber plants in the greenhouse,were characterized.Communities were analyzed by the quantity and diversity of their polymerase chain reaction(PCR)-amplified 16S rRNA genes.To account for TWW-associated nutrient effects,potable water(PW)served as a control.Amplicon sequence analysis showed that prokaryotic communities mainly consisted of bacteria(99.8%).Upon irrigation,regardless of the water quality,prokaryotic diversity declined,p H increased,and no bacterial growth was detected in bulk soil.In contrast,the growth of cucumbers was stimulated by TWW,indicating that plants were the main beneficiaries.Moreover,strong responses were seen in the rhizosphere,suggesting an indirect effect of TWW by altered rhizodepositions.The main bacterial responders to TWW were Proteobacteria,Bacteroidetes,Actinobacteria,and Planctomycetes.Changes in bacterial communities due to TWW were less pronounced in all variants of the silt loam,indicating the importance of clay and soil organic carbon for buffering effects of TWW on soil bacterial communities.Hence,soil organic carbon and soil texture are important parameters that need to be considered when applying TWW in agriculture.

Panax notoginseng saponins prevent colitis-associated colorectal cancer development: the role of gut microbiota

Gut microbiota dysbiosis is a risk factor for colorectal cancer(CRC) in inflammatory bowel disease(IBD).In this study, the effects of Panax notoginseng saponins(PNS) on colitis-associated CRC progression were evaluated on an azoxymethane(AOM)/dextran sulfate sodium(DSS) mouse model.In vivo, PNS significantly relieved AOM/DSS-induced colon tumorigenesis and development by reducing the disease activity index(DAI) scores and colon tumor load.The 16S rRNA data of fecal samples showed that the microbiome community was obviously destructed, while PNS could recover the richness and diversity of gut microbiota.Especially, PNS could increase the abundance of Akkermansia spp.which was significantly decreased in model group and negatively correlated with the progression of CRC.Moreover, ginsenoside compound K(GC-K) was evaluated on the effects of human CRC cells,which was the main bio-transformed metabolite of PNS by gut microbiota.Our data showed that PNS played important role in the prevention of the progression of CRC, due to their regulation on the microbiome balance and microbial bio-converted product with antiCRC activity.

Comparison of Composition and Diversity of Bacterial Microbiome in Human Upper and Lower Respiratory Tract

INTRODUCTIONMicrobiome residing in the airways and parenchymal tissues, as a biological barrier of respiratory tract, plays an important role in maintaining the normal functions of individual＇s respiratory system and preventing the invasion and colonization of exogenous pathogens.H1 Changes of microbial community may result in the occurrence and progression of infectious pneumonia and acute exacerbation of chronic diseases, through disordering commensal microorganisms and increasing invasive ability of pathogens.F21 Traditional methods for detecting bacteria normally rely on culture technique, which have a number of critical problems, including time-consuming and relatively low positive rate of detection. In the last 1 0 years, 16S rRNA gene sequencing technique has been thought to be more comprehensive and reliable than those of culture-dependent methods for monitoring bacterial microbiome in skin, organs, and tracts quantitatively and qualitatively.E31 In this case, choosing credible samples are critical to evaluate the community composition of microbiome in the host tracts, including respiratory tract. In the present study, we aimed to compare the composition and diversity of bacterial community structure in different samples collected from the individuals＇ airways using 16S rRNA gene sequencing technique.

Analysis of the relationship between bile duct and duodenal microbiota reveals that potential dysbacteriosis is the main cause of primary common bile duct stones

Bacteria play an important role in the formation of primary Common Bile Duct(CBD)stones.However,the composition and function of the microbiota of bile duct in patients with primary CBD stones remained to be explored.We utilized the 16S rRNA gene high-throughput sequencing technology to analyze the microbial diversity and community composition of biliary and duodenal microbiota in 15 patients with primary CBD stones and 4 patients without biliary tract diseases.Alpha diversity analysis showed that the microbiota richness was similar in bile and intestinal fluid;Beta diversity analysis showed that there were differences in the composition between biliary microbiota and the duodenal microbiota,but the abundance of the main groups showed similarities.The composition of the biliary microbiota from gallstone patients was more complex,as was the duodenal microbiota.Proteobacteria and Firmicutes were the dominant bacteria at phylum level,accounting for at least 75%of the total reads in each subgroup.Pseudomonas and EscherichiaShigella were the major genus among subgroups,but Escherichia-Shigella had increased abundance in duodenal microbiota with primary choledocholithiasis,which may play an important role in stone formation.It is noteworthy that Clostridiumsensu_stricto,Lachnospiraceae_UCG-008,Butyrivibrio and Roseburia which could produce short chain fatty acids(SCFAs),were significantly decreased in biliary microbiota with primary CBD stones(p<0.05).Our study provided new insights into the compositional of normal biliary microbiota.The micro-ecology of biliary and duodenal in patients with stones is complex and closely related,and there is a potential for dysbacteriosis.The decrease in abundance of certain major acid-producing bacteria affects the health of the biliary tract and thus leads to the formation of stones.