16S rRNA Gene-Based Metagenomic Analysis of Soil Bacterial Diversity in Brazzaville, Republic of the Congo

Soil contains a great diversity of microorganisms, among which are bacteria. This study aimed to explore bacterial diversity in soil samples in Brazzaville in the Republic of the Congo. Environmental DNA was extracted. The illumina MiSeq sequencing was held and the diversity indices have been computed. Illumina MiSeq sequencing revealed 21 Phyla, four of which were abundant: Proteobacteria, Acidobacteria, Actinobacteria and Bacteroidetes. Soil microbial communities in the studied samples were phylogenetically diverse but with a stable community structure. 17 classes are represented with relative abundances of Rihzobiales, Bacillales, Actinomycetales and Acidobacteriales. 40 families, the Alphaproteobacteria, the Bacilli and the 12 Actinobacteria. 83 orders among which the Rhizobiales are the most abundant followed by Bacillales and the least abundant followed by the Flavobacteriaceae. Of the 28 genera listed, the Bradyrhizobium is the most dominant in Mw3 and Mw4. 25 listed species, Bradyrhizobium, Bacillus, Actinoplanes, and Candidatu coribacter Acidobacterium are the most abundant species. The Shannon indices of Mw3 and Mw4 are equal, the H’max of Mw4 is greater than the H’max of Mw3. The Simpson index of Mw4 is equal to the Simpson index of Mw3, and the Pielou index (J) of Mw4 is less than the R of Mw3, but very close. This study opens interesting perspectives on the knowledge and exploitation of telluric bacteria in several areas of life.

Bacterial community structure in Apis florea larvae analyzed by denaturing gradient gel electrophoresis and 16S rRNA gene sequencing

This study characterizes the colonization and composition of bacterial flora in dwarf Asian honeybee （Apisflorea） larvae and compares bacterial diversity and distribu- tion among different sampling locations. A. florea larvae were collected from 3 locations in Chiang Mai province, Thailand. Bacterial DNA was extracted from each larva using the phenol-chloroform method. Denaturing gradient gel electrophoresis was performed, and the dominant bands were excised from the gels, cloned, and sequenced for bacterial species identification. The result revealed similarities of bacterial community profiles in each individual colony, but differences between colonies from the same and different locations. A. florea larvae harbor bacteria belonging to 2 phyla （Firmicutes and Proteobac- teria）, 5 classes （Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Bacilli, and Clostridia）, 6 genera （Clostridium, Gilliamella, Melissococcus, Lactobacillus, Saccha- ribacter, and Snodgrassella）, and an unknown genus from uncultured bacterial species. The classes with the highest abundance of bacteria were Alphaproteobacteria （34%）, Bacilli （25%）, Betaproteobacteria （11%）, Gammaproteobacteria （10%）, and Clostridia （8%）, re- spectively. Similarly, uncultured bacterial species were identified （12%）. Environmental bacterial species, such as Saccharibacterfloricola, were also found. This is the first study in which sequences closely related to Melissococcus plutonius, the causal pathogen re- sponsible for European foulbrood, have been identified in Thai A. florea larvae.

Analysis of the Microbiome Based on 16S rRNA Gene Signature in Women with Preterm versus Term Birth

Objective: To characterize and compare the microbiome signature in the maternal, intrauterine, and fetal environments and the associated bacterial species in women who experienced preterm birth and term birth.Methods: A total of 140 women with singleton pregnancies were enrolled in this study. Among them, 31 experienced spontaneous preterm delivery (gestational age < 37 weeks), and 28 of them experienced vaginal delivery at term. Maternal peripheral blood, saliva, and vaginal discharge samples and fetal membrane, amniotic fluid, and cord blood samples were collected immediately after delivery under sterile conditions. DNA was isolated from the fetal membrane and umbilical cord blood samples, and the V3-V4 region of the bacterial 16S rRNA gene was sequenced. The sequence data were quality-filtered, chimera-checked, and organized into operational taxonomic units (OTUs) based on phylogeny. Principal coordinate analysis of beta diversity measures was used for visualization. The linear discriminant analysis effect size (LEfSe) algorithm and Wilcoxon test were used to differentiate the microbiomes found in the fetal membranes and cord blood in the cases of preterm birth.Results: OTU analysis based on the 16S rRNA gene showed similar microbiomes in the maternal peripheral blood, amniotic fluid, fetal membranes, and cord blood. However, the LEfSe algorithm revealed significantly different bacterial compositions in the fetal environment between the preterm and term groups, with some of the bacterial species originating from the maternal peripheral blood or saliva.Conclusions: The bacteria in the intrauterine and fetal environments may originate from other body sites through hematogenous transmission, and may cause the occurrence of preterm birth.

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.

Development of a 16S r RNA gene-based microarray for the detection of marine bacterioplankton community

A better understanding of bacterioplankton community shifts following change in marine environments is critical to predict the marine ecosystem function. In order to get a snapshot of the microbial taxonomy profiling of a wide range marine area, a quick, convenient and low cost method would be favorable. In this study, we developed a 16S rRNA gene-based microarray using ARB software, which contained 447 probes targeting 160 families of marine bacteria. The specificity, sensitivity and quantitative capability of this microarray were assessed by single cloned16S rRNA genes. The reliability of this microarray was tested by eight environmental samples. The results showed that the microarray was specific, only 1.16% false results were detected in five single-clone hybridization tests. The microarray could detect DNA samples as few as 1 ng/μL and the signal intensity could reflect the relative abundance of the bacteria in the range of 1 ng/μL to 100 ng/μL of DNA concentration. Hybridization with environmental samples showed that it can discriminate bacterioplankton communities by sites and time. High throughput sequencing results from the eight samples confirmed the hybridization results. It indicated that this developed microarray could be used as a convenient tool to monitor the bacterioplankton community in marine environment.

Phylogenetic diversity of planktonic bacteria in the Chukchi Borderland region in summer

Planktonic bacteria are abundant in the Chukchi Borderland region. However, little is known about their di- versity and the roles of various bacteria in the ocean. Seawater samples were collected from two stations K2S and K4S where sea ice was melting obviously. The analysis of water samples with fluorescence in situ hybridization （FISH） showed that DMSP-degrading bacteria accounted for 13% of the total bacteria at the station K2S. No aerobic anoxygenic phototrophic （AAP） bacteria were detected in both samples. The bacterial communities were characterized by two 16S rRNA gene clone libraries. Sequences fell into four major lineages of the domain Bacteria, including Proteobacteria （Alpha, Beta and Gamma subclasses）, Bac- teroidetes, Actinobacteria and Firmicutes. No significant difference was found between the two clone li- braries. SAR11 and Rhodobacteraceae clades of Alphaproteobacteria and Pseudoalteromonas of Gammapro- teobacteria constituted three dominant fractions in the clone libraries. A total of 191 heterotrophic bacterial strains were isolated and 76% showed extracellular proteolytic activity. Phylogenetic analysis reveals that the isolates fell into Gammaproteobacteria, Bacteroidetes, Actinobacteria and Firmicutes. The most common genus in both the bacterial isolates and protease-producing bacteria was Pseudoalteromonas. UniFrac data showed suggestive differences in bacterial communities between the Chukchi Borderland and the northern Bering Sea.

Microbial community structure and nitrogenase gene diversity of sediment from a deep-sea hydrothermal vent field on the Southwest Indian Ridge

A sediment sample was collected from a deep-sea hydrothermal vent field located at a depth of 2 951 m on the Southwest Indian Ridge. Phylogenetic analyses were performed on the prokaryotic community using polymerase chain reaction（PCR） amplification of the 16 S rRNA and nifH genes. Within the Archaea, the dominant clones were from marine benthic group E（MBGE） and marine group I（MGI） belonging to the phyla Euryarchaeota and Thaumarchaeota, respectively. More than half of the bacterial clones belonged to the Proteobacteria, and most fell within the Gammaproteobacteria. No epsilonproteobacterial sequence was observed. Additional phyla were detected including the Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Nitrospirae, Chloroflexi, Chlorobi, Chlamydiae, Verrucomicrobia, and candidate divisions OD1, OP11, WS3 and TM6, confirming their existence in hydrothermal vent environments. The detection of nifH gene suggests that biological nitrogen fixation may occur in the hydrothermal vent field of the Southwest Indian Ridge. Phylogenetic analysis indicated that only Clusters I and III NifH were present. This is consistent with the phylogenetic analysis of the microbial 16 S rRNA genes, indicating that Bacteria play the main role in nitrogen fixation in this hydrothermal vent environment.

Sizes of Anode and Cathode Affect Electricity Generation in Rice Paddy-Field Microbial Fuel Cells

Rice paddy-field microbial fuel cells (RPF-MFCs) are devices that exploit rhizosphere bacteria to generate electricity from soil organic matter, including those excreted from roots. Previous studies have examined factors affecting electric outputs from RPF-MFCs and demonstrated that RPFMFC was able to generate electricity up to 80 mW·m-2 (based on the projected area of anode). The present study operated RPF-MFCs with different sizes of anodes and cathodes and examined how electrode sizes affected electricity generation. We show that anodes are the limiting factor for electricity generation immediately after commencing the operation, while cathodes become the limiting factor after anode performances are sufficiently increased. RPF-MFC achieved the maximum power density of 140 mW·m-2 (based on the projected area of anode), when the cathode is sufficiently larger than the anode. Results suggest that the cathode needs to be improved for eliciting the maximum capacity of rhizosphere bacteria for electricity generation in RPF-MFC.

Impact of preoperative antibiotics and other variables on integrated microbiome-host transcriptomic data generated from colorectal cancer resections

BACKGROUND Integrative multi-omic approaches have been increasingly applied to discovery and functional studies of complex human diseases.Short-term preoperative antibiotics have been adopted to reduce site infections in colorectal cancer(CRC)resections.We hypothesize that the antibiotics will impact analysis of multi-omic datasets generated from resection samples to investigate biological CRC risk factors.AIM To assess the impact of preoperative antibiotics and other variables on integrated microbiome and human transcriptomic data generated from archived CRC resection samples.METHODS Genomic DNA(gDNA)and RNA were extracted from prospectively collected 51 pairs of frozen sporadic CRC tumor and adjacent non-tumor mucosal samples from 50 CRC patients archived at a single medical center from 2010-2020.The 16S rRNA gene sequencing(V3V4 region,paired end,300 bp)and confirmatory quantitative polymerase chain reaction(qPCR)assays were conducted on gDNA.RNA sequencing(IPE,125 bp)was performed on parallel tumor and non-tumor RNA samples with RNA Integrity Numbers scores≥6.RESULTS PERMANOVA detected significant effects of tumor vs nontumor histology(P=0.002)and antibiotics(P=0.001)on microbialβ-diversity,but CRC tumor location(left vs right),diabetes mellitus vs not diabetic and Black/African Ancestry(AA)vs not Black/AA,did not reach significance.Linear mixed models detected significant tumor vs nontumor histology*antibiotics interaction terms for 14 genus level taxa.QPCR confirmed increased Fusobacterium abundance in tumor vs nontumor groups,and detected significantly reduced bacterial load in the(+)antibiotics group.Principal coordinate analysis of the transcriptomic data showed a clear separation between tumor and nontumor samples.Differentially expressed genes obtained from separate analyses of tumor and nontumor samples,are presented for the antibiotics,CRC location,diabetes and Black/AA race groups.CONCLUSION Recent adoption of additional preoperative antibiotics as standard of care,has a measurable impact on-omics analysis of resected specimens.This study still confirmed increased Fusobacterium nucleatum in tumor.

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.

Encapsulated peracetic acid as a valid broad‑spectrum antimicrobial alternative,leading to beneficial microbiota compositional changes and enhanced performance in broiler chickens

Background Antimicrobial alternatives are urgently needed,including for poultry production systems.In this study,we tested the potential broad-range antimicrobial alternative peracetic acid,delivered in feed via the hydrolysis of encapsulated precursors through a 28-day study using 375 Ross 308 broiler chickens.We tested two peracetic acid concentrations,30 and 80 mg/kg on birds housed on re-used litter,and we evaluated the impact of both levels on gut microbial communities,bacterial concentration,antimicrobial resistance genes relative abundance and growth performance when compared to control birds housed on either clean or re-used litter.Results Body weight gain and feed conversion ratio improved in peracetic acid fed birds.At d 28,birds given 30 mg/kg of peracetic acid had a decreased Firmicutes and an increased Proteobacteria abundance in the jejunum,accompanied by an increase in Bacillus,Flavonifractor and Rombustia in the caeca,and a decreased abundance of tetracycline resistance genes.Chicken given 80 mg/kg of peracetic acid had greater caecal abundance of macrolides lincosamides and streptogramins resistance genes.Growth performance on clean litter was reduced compared to reused litter,which concurred with increased caecal abundance of Blautia,decreased caecal abundance of Escherichia/Shigella,Anaerostipes and Jeotgalicoccus,and greater gene abundance of vancomycin,tetracycline,and macrolides resistance genes.Conclusions Peracetic acid could be used as a safe broad-spectrum antimicrobial alternative in broilers.Encapsulated precursors were able to reduce the bacterial concentration in the jejunum whilst promoting the proliferation of probiotic genera in the caeca,especially at the low peracetic acid concentrations tested,and improve growth performance.Moreover,our findings offer further insights on potential benefits of rearing birds on re-used litter,suggesting that the latter could be associated with better performance and reduced antimicrobial resistance risk compared to clean litter rearing.

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.

Comparison of genomic and transcriptional microbiome analysis in gastric cancer patients and healthy individuals

BACKGROUND Helicobacter pylori and the stomach microbiome play a crucial role in gastric carcinogenesis,and detailed characterization of the microbiome is necessary for a better understanding of the pathophysiology of the disease.There are two common modalities for microbiome analysis:DNA(16S rRNA gene)and RNA(16S rRNA transcript)sequencing.The implications from the use of one or another sequencing approach on the characterization and comparability of the mucosal microbiome in gastric cancer(GC)are poorly studied.AIM To characterize the microbiota of GC using 16S rRNA gene and its transcript and determine difference in the bacterial composition.METHODS In this study,316 DNA and RNA samples extracted from 105 individual stomach biopsies were included.The study cohort consisted of 29 healthy control individuals and 76 patients with GC.Gastric tissue biopsy samples were collected from damaged mucosa and healthy mucosa at least 5 cm from the tumor tissue.From the controls,healthy stomach mucosa biopsies were collected.From all biopsies RNA and DNA were extracted.RNA was reverse transcribed into cDNA.V1-V2 region of bacterial 16S rRNA gene from all samples were amplified and sequenced on an Illumina MiSeq platform.Bray-Curtis algorithm was used to construct sample-similarity matrices abundances of taxonomic ranks in each sample type.For significant differences between groups permutational multivariate analysis of variance and Mann-Whitney test followed by false-discovery rate test were used.RESULTS Microbial analysis revealed that only a portion of phylotypes(18%-30%)overlapped between microbial profiles obtained from DNA and RNA samples.Detailed analysis revealed differences between GC and controls depending on the chosen modality,identifying 17 genera at the DNA level and 27 genera at the RNA level.Ten of those bacteria were found to be different from the control group at both levels.The key taxa showed congruent results in various tests used;however,differences in 7 bacteria taxa were found uniquely only at the DNA level,and 17 uniquely only at the RNA level.Furthermore,RNA sequencing was more sensitive for detecting differences in bacterial richness,as well as differences in the relative abundance of Reyranella and Sediminibacterium according to the type of GC.In each study group(control,tumor,and tumor adjacent)were found differences between DNA and RNA bacterial profiles.CONCLUSION Comprehensive microbial study provides evidence for the effect of choice of sequencing modality on the microbiota profile,as well as on the identified differences between case and control.

Prokaryotic diversity and community composition in the surface sediments of the Changjiang River Estuary in summer

Microorganisms are fundamental for the functioning of marine ecosystems and are involved in the decomposition of organic matter, transformation of nutrients and circulation of biologically-important chemicals. Based on the complexity of the natural geographic characteristics of the Changjiang River Estuary, the geographic distribution of sedimentary microorganisms and the causes of this distribution are largely unexplored. In this work, the surface sediment samples from the adjacent sea area of the Changjiang River Estuary were collected. Their prokaryotic diversity was examined by high-throughput sequencing technology, and the environmental factors of the bacterial community were investigated. The results indicated that the distribution of prokaryotic communities in the sediments of the study areas showed obvious spatial heterogeneity. The sampling sequences divided the sample regions into three distinct clusters. Each geographic region had a unique community structure, although Proteobacteria, Bacteroidota, Desulfobacterota, Acidobacteriota, and Actinobacteriota all existed in these three branches. Canonical correspondence analysis demonstrated that prokaryotic diversity and community distribution were significantly correlated with the geographic location of sediment, seawater depth, and in particular, nutrient content(e.g., total phosphorus, total organic carbon and dissolved oxygen). Moreover, it was found for the first time that the metal ions obviously affected the composition and distribution of the prokaryotic community in this area. In general, this work provides new insights into the structural characteristics and driving factors of prokaryotic communities under the background of the ever-changing Changjiang River Estuary.

RETRACTED:Effect of Long-Term Inorganic Fertilization on Diversity and Abundance of Bacterial and Archaeal Communities at Tillage in Irrigated Rice Field

Short Retraction Notice The paper does not meet the standards of "Advances in Bioscience and Biotechnology". This article has been retracted to straighten the academic record. In making this decision the Editorial Board follows COPE's Retraction Guidelines. The aim is to promote the circulation of scientific research by offering an ideal research publication platform with due consideration of internationally accepted standards on publication ethics. The Editorial Board would like to extend its sincere apologies for any inconvenience this retraction may have caused. Editor guiding this retraction: Prof. Abass Alavi (EiC of ABB). Please see the article page for more details. The full retraction notice in PDF is preceding the original paper which is marked "RETRACTED".

PCR-DGGE法分析不同酒曲中细菌多样性

目的:研究不同酒曲中细菌的多样性.方法:利用DNA提取试剂盒,分别提取6种酒曲的总DNA,利用细菌16S rRNA gene V3区通用引物,采用变性梯度凝胶电泳(polymerase chain reaction-denatured gradient gelelectrophoresis,PCR-DGGE)方法,进行不同酒曲中细菌多样性的分析.结果:6种酒曲中共分离出12属的细菌,分别为:湖南韶山的酒曲中主要是Weissella,Streptophyta,Bacillus,Pantoea,Okibacterium这5个属的菌株,湖南湘潭酒曲中主要含有Weissella,Pediococcus,Lactococcus,Sphingomonas,Streptophyta,Pantoea这6属的菌株,湖南祁东酒曲中主要含有Weissella,Pediococcus,Bacillus,Klebsiella,Pantoea 5属的菌株,福建福州酒曲含有Weissella,Pediococcus,Pantoea,Pediococcus,Sphingomonas,Streptophyta 6属的菌株,浙江丽水酒曲含有Weissella,Pantoea,Pediococcus,Klebsiella,Enterobacter,Rhizobium,Sphingomonas,Thauera 8属的菌株,浙江兰溪酒曲含有Weissella,Streptophyta,Pantoea 3属的菌株.结论:这说明不同地区的酒曲中的细菌的种类有所不同,同时也说明酒曲中Weissella属的菌是发酵的常见菌群.

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.

Cultivation-Independent Analysis of the Development of the Lactobacillus spp.Community in the Intestinal Tract of Newborn Piglets

Molecular diversity and development of the Lactobacillus community in the intestinal tract, as influenced by age and intestinal compartment, were studied in one litter of 12 conventionally raised piglets. Piglets were euthanized at each week （3 animals per time）. Digesta and tissue samples from stomach, duodenum, jejunum, ileum, caecum, colon, and rectum were collected and analysed by using 16S ribosomal RNA-based methods. DGGE （denaturing gradient gel electrophoresis） profiles revealed that the Lactobacillus communities throughout the GI tract from duodenum to rectum showed good stability at same age. This indicates that fecal Lactobacillus communities can effectively represent the intestinal community. Two dominant bands were found in tissue samples of the small intestine, suggesting that the lactobacilli can adhere to the small intestinal wall. The Lactobacillus communities in different GI tract compartments developed over time. A successional change of Lactobacillus communities was observed from birth, through creep feeding to one week after weaning, showing a trend from simple to complex and back to simple. Furthermore, a clone library of Lactobacillus spp. 16S rRNA gene sequences were generated from jejunal and colonic chymes. Six dominant DGGE bands generated from jejunal chymes were matched with sequences that show 94-98% similarity to the bands derived from L. reuteri, L. delbrueckii, and L. crispatus. Seven dominant DGGE bands generated from colon chymes were matched with sequences that show 88-99% similarity to those derived from L. reuteri, L. delbrueckii, L. amylovorus/L. sobrius, and L. acidophilus. Amplicons related to L. reuteri were found in all DGGE fingerprints from jejunal digesta of age of weeks 1, 3, and 4. Amplicons related to L. amylovorus/L. sobrius were present in all DGGE fingerprints from colonic digesta of age of week 1, 3, and 4. Amplicons related to L. delbrueckii were found before weaning, L. crispatus after creep feeding before weaning and L. acidophilus after weaning. This indicates that L. reuteri and L. amylovorus/L. sobrius probably belong to the permanent composition, while L. delbruckii, L. acidophilus, and L. crispatus probably belong to the temporal groups of Lactobacillus communities in the GI tract of piglets.

Quantitative comparisons of select cultured and uncultured microbial populations in the rumen of cattle fed different diets

Background： The number and diversity of uncultured ruminal bacterial and archaeal species revealed by 16S rRNA gene firs） sequences greatly exceeds that of cultured bacteria and archaea. However, the significance of uncultured microbes remains undetermined. The objective of this study was to assess the numeric importance of select uncultured bacteria and cultured bacteria and the impact of diets and microenvironments within cow rumen in a comparative manner. Results： Liquid and adherent fractions were obtained from the rumen of Jersey cattle fed hay alone and Holstein cattle fed hay plus grain. The populations of cultured and uncultured bacteria present in each fraction were quantified using specific real-time PCR assays. The population of total bacteria was similar between fractions or diets, while total archaea was numerically higher in the hay-fed Jersey cattle than in the hay-grain-fed Holstein cattle. The population of the genus Prevotello was about one log smaller than that of total bacteria. The populations of Fibrobocter succinogenes, Ruminococcus flovefociens, the genus Butyrivibrio, and R. albus was at least one log smaller than that of genus Prevotello. Four of the six uncultured bacteria quantified were as abundant as F. succinogenes, R. flovefociens and the genus Butyrivibrio. In addition, the populations of several uncultured bacteria were significantly higher in the adherent fractions than in the liquid fractions. These uncultured bacteria may be associated with fiber degradation. Conclusions： Some uncultured bacteria are as abundant as those of major cultured bacteria in the rumen. Uncultured bacteria may have important contribution to ruminal fermentation. Population dynamic studies of uncultured bacteria in a comparative manner can help reveal their ecological features and importance to rumen functions.

Microbial community structure and diversity in deep-sea hydrothermal vent sediments along the Eastern Lau Spreading Centre

The aim of this study is to investigate microbial structures and diversities in five active hydrothermal fields＇ sediments along the Eastern Lau Spreading Centre （ELSC） in the Lau Basin （southwest Pacific）. Microbial communities were surveyed by denatured gradient gel electrophoresis （DGGE） and clone library analysis of 16S rRNA genes. The differences in microbial community structures among sediment samples from the five deep-sea hydrothermal sites were revealed by DGGE profiles. Cluster analysis of DGGE profiles sepa- rated the five hydrothermal samples into two groups. Four different 16S rRNA gene clone libraries, repre- senting two selected hydrothermal samples （19-4TVG8 and 19-4TVG11）, were constructed. Twenty-three and 32 phylotypes were identified from 166 and 160 bacterial clones respectively, including Proteobacteria, Bacteroidetes, Firmicutes, Nitrospirae and Planctomycetes. The phylum Proteobacteria is dominant in both bacterial libraries with a predominance of Gamma-Proteobacteria. A total of 31 and 25 phylotypes were obtained from 160 and 130 archaeal clones respectively, including Miscellaneous Crenarchaeotic Group, Marine Group Ⅰ and Ⅲ, Marine Benthic Group E, Terrestrial Hot Spring Crenarchaeota and Deep-sea Hy- drothermal Vent Euryarchaeota. These results show a variety of clones related to those involved in sulfur cycling, suggesting that the cycling and utilization of sulfur compounds may extensively occur in the Lau Basin deep-sea hydrothermal ecosystem.