Fecal microbiota of three bactrian camels(Camelus ferus and Camelus bactrianus) in China by high throughput sequencing of the V3-V4 region of the 16S rRNA gene

This study aimed to reveal the microbial diversity in the fecal samples of bactrian camels using the 16 S r RNA sequencing analysis on the Illumina Mi Seq platform. Three fecal samples were collected from two geographical regions in China. Operational taxonomic unit（OTU） clustering was performed by identifying an OTU at 97% sequence identity. The alpha and beta diversities were applied to estimate the differences in microbial diversity among the three fecal samples. Totally, 4409, 3151 and 4075 OTUs in the fecal samples were identified in the Lop Nor wild camel（Camelus ferus）, the domestic camel（C. bactrianus） and Dunhuang wild camel（C. ferus）, respectively. The majority of bactreria were affiliated with phylum Firmicutes and Bacteroidetes in the three samples. The wild camels had higher gastrointestinal tract microbial diversity than the domestic one, while the microbial composition of the Lop Nor wild camel shared higher similarity with domestic camel at the genus and family levels than that of the Dunhuang wild camel did. Our results may provide a theoretical basis for assessing their health conditions and may thus be useful for protecting the critically endangered species of C. ferus.

Correlation analysis of breast fibroadenoma and the intestinal flora based on 16S rRNA sequencing

Objective To analyze the characteristics of the intestinal microflora in patients with breast fibroadenoma using 16S ribosomal RNA(rRNA)high-throughput sequencing.Methods Fecal samples from 20 patients with breast fibroadenoma and 36 healthy subjects were randomly collected and analyzed using high-throughput sequencing technology for 16S rRNA V4 region sequencing,and the alpha diversity(Chao index,Shannon index)was calculated using Mothur(v.1.39.5)software.Beta diversity was analyzed using QIIME(v1.80).SPSS software(version 23.0)and the t-test of two independent samples were used to analyze differences in the abundance of bacteria between the two groups.Results Compared with that in the healthy control group,theαdiversity of the intestinal microflora in breast fibroadenoma patients increased,but the difference was not statistically significant(P>0.05).At the phylum level,significant differences were observed between the two groups.The abundance of Firmicutes was higher in the breast fibroadenoma group(P<0.05),whereas the abundance of Synergistetes was higher in the healthy control group(P<0.005).A total of five bacterial genera showed significant differences between the two groups:the breast fibroadenoma group showed higher levels of Bautia(P<0.005),Coprococcus(P<0.005),Roseburia(P<0.05),and Ruminococcus(P<0.005),whereas Sutterella was more abundant in the healthy control group than in the breast fibroadenoma group(P<0.05).Conclusion The diversity and abundance of the intestinal flora in patients with breast fibroadenoma are significantly different from those in healthy subjects,suggesting that an imbalance in the intestinal flora is correlated with the occurrence of breast fibroadenoma.

From Phenotypes to Molecules: Revolutionizing Gut Microbiota Identification Methods

The gut microbiota is a complex ecosystem composed of many bacteria and their metabolites.It plays an irreplaceable role in human digestion,nutrient absorption,energy supply,fat metabolism,immune regulation,and many other aspects.Exploring the structure and function of the gut microbiota,as well as their key genes and metabolites,will enable the early diagnosis and auxiliary diagnosis of diseases,new treatment methods,better effects of drug treatments,and better guidance in the use of antibiotics.The identification of gut microbiota plays an important role in clinical diagnosis and treatment,as well as in drug research and development.Therefore,it is necessary to conduct a comprehensive review of this rapidly evolving topic.Traditional identification methods cannot comprehensively capture the diversity of gut microbiota.Currently,with the rapid development of molecular biology,the classification and identification methods for gut microbiota have evolved from the initial phenotypic and chemical identification to identification at the molecular level.This review integrates the main methods of gut microbiota identification and evaluates their application.We pay special attention to the research progress on molecular biological methods and focus on the application of high-throughput sequencing technology in the identification of gut microbiota.This revolutionary method for intestinal flora identification heralds a new chapter in our understanding of the microbial world.

Vertical microbial profiling of water column reveals prokaryotic communities and distribution features of Antarctic Peninsula

Prokaryotic diversity and community composition in the water column of eight stations(63 samples) around the Antarctic Peninsula of the Southern Ocean were investigated. Through pyrosequencing of the V3–V4hypervariable regions of the 16S ribosomal RNA gene, we characterized 4 720 089 valid reads representing 48 188operational taxonomic units(OTUs, 97% similarity). The community was dominated by the phyla Pseudomonadota(original name: Proteobacteria, 47%), Oxyphotobacteria(26%), and Bacteroidota(original name: Bacteroidetes, 18%), which comprised an average of 91% of the total OTUs in all samples. The prokaryotic community composition varied vertically within the water column. Water column prokaryotic communities exhibited a clear depth profile, with higher microbial richness and higher diversity observed with increasing water depth. Cluster analysis of the community composition of water column samples exhibited a similar trend with depth. Correlation with environmental factors suggested distinct variation in prokaryotic community composition with changes in depth, salinity, temperature and dissolved oxygen levels. Functional prediction showed presence of active nitrogen, sulphur and methane metabolic cycles along the vertical transect of the studied region. These results will improve our knowledge of prokaryotic diversity and community composition at different depth of water column for better understanding of the microbial ecology and nutrient cycles in Antarctic Peninsula region of the Southern Ocean.

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.

血清凝集、基因测序联合检测群霍乱弧菌的应用

目的：避免霍乱弧菌检测假阳性，提高检测正确率。方法随机选取2013年1～7月，全国各省市 CDC 送往中国CDC 霍乱初筛阳性菌株14株；用 LB 营养琼脂培养12 h，挑取单菌落进行霍乱弧菌血清凝集，同时水煮模板法提取菌株的DNA。针对弧菌属16SrDNA 序列设计引物，进行弧菌16SrDNA PCR 检测，电泳观察16SrDNA 产物，将16SrDNA 阳性产物送测序公司测序，测序结果在 NCBI 网站上进行 Blast 比对，分析比较血清凝集和 Blast 比对结果。结果共选取14株菌进行实验，血清凝集阳性12株，2株未凝。经弧菌16SrDNA 扩增，电泳观察14株菌均扩增出相应的片段，说明所选菌株均为弧菌属。将14株菌的16SrDNA 阳性产物测序，并将测序结果进行 Blast 比对：2株血清未凝集菌均是哈维氏弧菌；12株血清凝集阳性的菌中，1株是需钠弧菌，其余11株是霍乱弧菌。结论血清凝集和基因测序联合检测群霍乱弧菌，可避免霍乱弧菌检测假阳性，提高检测正确率。

Faecal and mucosal microbiota in patients with functional gastrointestinal disorders: Correlation with toll-like receptor 2/toll-like receptor 4 expression

AIM To investigate the intestinal luminal microbiota(LM)and mucosa-associated microbiota(MAM)in Chinese patients with functional gastrointestinal disorders(FGIDs)and examine the association between these communities and the expression of toll-like receptor(TLR)2 and TLR4. METHODS Thirty-two Chinese subjects who suffered from symptoms of FGIDs,as confirmed by gastroenterologists,were enrolled in this study.Fresh faecal samples and descending colonic mucosal biopsies were collected from the subjects before(faecal)and during(mucosal) flexible colonoscopy.For analysis of the samples,we performed high-throughput sequencing of the V3-V4region of the 16S rR NA gene and reverse transcription(RT)-PCR to detect the expression of colonic TLR2 and TLR4.Differences in the stool and mucosal microbiota were examined and a correlation network analysis was performed. RESULTS The microbiota of faecal samples was significantly more diverse and richer than that of the mucosal samples,and the LM and MAM populations differed significantly.TLR2 expression showed a significant positive correlation with TLR4 expression.In the MAM samples,the genera Faecalibacterium and Ruminococcus,which belong to the family Ruminococcaceae,were inversely correlated with TLR4 expression(r=-0.45817,P=0.0083 and r=-0.5306,P=0.0018,respectively).Granulicatella,which belongs to Carnobacteriaceae,and Streptococcus,which belongs to Streptococcaceae,were inversely correlated with TLR2 expression(r=-0.5573,P=0.0010 and r=-0.5435,P=0.0013,respectively).In the LM samples,examination at phylum,class,or order level revealed no correlation with TLR4 expression.Faecalibacterium,which belongs to Ruminococcaceae,and Streptococcus,which belongs to Streptococcaceae,were inversely correlated with TLR2 expression(r=-0.5743,P=0.0058 and r=-0.3905,P=0.0271,respectively). CONCLUSION Microbial compositions of LM and MAM in Chinese patients with FGIDs are different.Expression of TLRs may be affected by the type of bacteria that are present in the gut.

Inhibition effect of magnetic field on nitrous oxide emission from sequencing batch reactor treating domestic wastewater at low temperature

This study aims to investigate the effect of a magnetic field on nitrous oxide(N2O)emission from a sequencing batch reactor treating low-strength domestic wastewater at low temperature(10℃).After running for 124 days in parallel,results indicated that the conversion rate of N2O for a magnetic field-sequencing batch reactor(MF-SBR)decreased by34.3%compared to that of a conventional SBR(C-SBR).Meanwhile,the removal efficiencies for total nitrogen(TN)and ammonia nitrogen(NH4-N)of the MF-SBR were 22.4%and 39.5%higher than those of the C-SBR.High-throughput sequencing revealed that the abundances of AOB(Nitrosomonas),NOB(Nitrospira)and denitrifiers(Zoogloea),which could reduce N2O to N2,were promoted significantly in the MF-SBR.Enzyme activities(Nir)and gene abundances(nos Z nir S and nir K)for denitrification in the MF-SBR were also notably higher compared to C-SBR.Our study shows that application of a magnetic field is a useful approach for inhibiting the generation of N2O and promoting the nitrogen removal efficiency by affecting the microbial characteristics of sludge in an SBR treating domestic wastewater at low temperature.

Oral microbiome and pancreatic cancer

BACKGROUND Microbiota profiles differ between patients with pancreatic cancer and healthy people,and understanding these differences may help in early detection of pancreatic cancer.Saliva sampling is an easy and cost-effective way to determine microbiota profiles compared to fecal and tissue sample collection.AIM To investigate the saliva microbiome distribution in patients with pancreatic adenocarcinoma(PDAC)and the role of oral microbiota profiles in detection and risk prediction of pancreatic cancer.METHODS We conducted a prospective study of patients with pancreatic cancer(n=41)and healthy individuals(n=69).Bacterial taxa were identified by 16S ribosomal ribonucleic acid gene sequencing,and a linear discriminant analysis effect size algorithm was used to identify differences in taxa.Operational taxonomic unit values of all selected taxa were converted into a normalized Z-score,and logistic regressions were used to calculate risk prediction of pancreatic cancer.RESULTS Compared with the healthy control group,carriage of Streptococcus and Leptotrichina(z-score)was associated with a higher risk of PDAC[odds ratio(OR)=5.344,95%confidence interval(CI):1.282-22.282,P=0.021 and OR=6.886,95%CI:1.423-33.337,P=0.016,respectively].Veillonella and Neisseria(z-score)were considered a protective microbe that decreased the risk of PDAC(OR=0.187,95%CI:0.055-0.631,P=0.007 and OR=0.309,95%CI:0.100-0.952,P=0.041,respectively).Among the patients with PDAC,patients reporting bloating have a higher abundance of Porphyromonas(P=0.039),Fusobacterium(P=0.024),and Alloprevotella(P=0.041);while patients reporting jaundice had a higher amount of Prevotella(P=0.008);patients reporting dark brown urine had a higher amount of Veillonella(P=0.035).Patients reporting diarrhea had a lower amount of Neisseria and Campylobacter(P=0.024 and P=0.034),and patients reporting vomiting had decreased Alloprevotella(P=0.036).CONCLUSION Saliva microbiome was able to distinguish patients with pancreatic cancer and healthy individuals.Leptotrichia may be specific for patients living in Sichuan Province,southwest China.Symptomatic patients had different bacteria profiles than asymptomatic patients.Combined symptom and microbiome evaluation may help in the early detection of pancreatic cancer.

Spatial distribution characteristics of bacterial community structure and gene abundance in sediments of the Bohai Sea

This study investigated differences in the community structure and environmental responses of the bacterial community in sediments of the Bohai Sea.Illumina high-throughput sequencing technology and real-time PCR were used to assay the bacterial 16S rRNA genes in the surface sediments of 13 sampling stations in the Bohai Sea.The results showed that sediments at the majority of the 13 sampling stations were contaminated by heavy metal mercury.The main phyla of bacteria recorded included Proteobacteria(52.92%),Bacteroidetes(11.76%),Planctomycetes(7.39%),Acidobacteria(6.53%)and Chloroflexi(4.97%).The genus with the highest relative abundance was Desulfobulbus(4.99%),which was the dominant genus at most sampling stations,followed by Lutimonas and Halioglobus.The main factors influencing bacterial community structure were total organic carbon,followed by depth and total phosphorus.The content of lead,cadmium,chromium,copper and zinc had a consistent effect on community structure.Arsenic showed a negative correlation with bacterial community structure in most samples,while the impact of mercury on community structure was not significant.The bacterial community in sediment samples from the Bohai Sea was rich in diversity and displayed an increase in diversity from high to low latitudes.The data indicated that the Bohai Sea had abundant microbial resources and was rich in bacteria with the potential to metabolize many types of pollutants.

Distribution and diversity of microbial communities in meromictic soda Lake Doroninskoe(Transbaikalia,Russia) during winter

Meromictic soda and saline lakes are unique ecosystems characterized by the stability of physical,chemical and biological parameters,and they are distributed all over the world.Lakes located in regions with average annual negative air temperature are of particular interest because of the presence of two periods with intensive and dynamic processes:the so-called biological summer and the long ice season with the biological spring.Soda Lake Doroninskoe is located in Eastern Transbaikalia(51°14′N,112°14′E) in the permafrost zone in an extreme continental climate,and is covered by ice for seven months per year.The structure and diversity of the microbial communities throughout the water column of the lake was studied by 16 S r RNA gene amplicon metasequencing.Different species with specific functions were found to dominate at different depths.Metabolically flexible bacteria with a capacity to switch between anoxygenic photosynthesis and aerobic chemotrophic metabolism dominate in soda Lake Doroninskoe.

Characterization of microbial communities in sediments of the South Yellow Sea

Illumina sequencing and quantitative PCR(qPCR)based on the 16 S ribosomal RNA(rRNA)gene were conducted to characterize the vertical distribution of bacterial and archaeal communities in the sediments of two sites from the South Yellow Sea.Both bacterial and archaeal communities showed a clear stratified distribution with sediment depth.The microbial communities in the upper layers were distinct from those in the deeper layers;the relative abundances of sequences of Thaumarchaeota,Gammaproteobacteria,and Actinobacteria were higher in the upper than in the deeper sediments,whereas the sequences of Bathyarchaeia,Lokiarchaeota,Euryarchaeota,Chloroflexi,and Deltaproteobacteria were relatively more abundant in the deeper sediments.Sediment depth and total organic carbon(TOC)can significantly influence both the bacterial and archaeal communities.Furthermore,bacterial and archaeal groups potentially involved in nitrogen,sulfur,and methane metabolism were detected in both sites.In our study,both ammonia-oxidizing bacteria(Nitrospira)and ammonia-oxidizing archaea(Candidatus Nitrosopumilus)were responsible for ammonia oxidization.Additionally,sulfur-reducing bacteria SEEP-SRB1 forming consortia with anaerobic methane-oxidizing archaea ANME-2 a-2 b were capable of anaerobic methane oxidation(AOM)in the 3400-02 sediment samples.

Response of Heterotrophic Bacteria Abundance and Community Structure to Asian Dust Addition in the Oligotrophic Northwest Pacific Ocean

The dust storms from the continent usually affect the abundance and diversity of planktons by supplying trace elements. As such, the response of heterotrophic planktonic bacteria to dusts, nutrients(i.e., nitrogen and phosphorus) or ferrous dosages was investigated in the Kuroshio Extension region of the Northwest Pacific Ocean(NWPO) through on-board incubation experiments during an oceanographic survey in spring 2014. The flow cytometry and 16S rRNA high-throughput sequencing methods were applied to explore the abundance and community structure of bacteria, and the percentage of high nucleic acid bacteria(HNA%). The results showed that the heterotrophic bacteria abundance was low(average 2.55×10^5 cells mL^-1) and subjected to both nitrogen(N) and ferrous(Fe) limitation. Sand-dust deposition observably promoted the activity of heterotrophic planktonic bacteria. The maximum abundance of heterotrophic bacteria was 6.98×10^5 cells mL^-1 in the dust-dosage group, which was 44% higher than the control(P < 0.05). The HNA% in the dust-dosage group was 1.37 times higher than the control(P < 0.05). The activation mechanism was mainly related to the dissolution of N and Fe in the dusts. The relative abundance of genus Winogradskyella was significantly increased by dust deposition while the relative abundance of the genera Tenacibaculum and Hyphomonas was decreased. These variations of bacterial community structure were ascribed to the dissolution of nutrients N and P. Comparing the results of different experimental groups, this study concluded that dust storm improved the abundance of heterotrophic bacteria by dissolution of N and Fe.

Ganjiang granule regulates cecal microflora and serum biochemical components in a rat model of constipation-predominant irritable bowel syndrome

Objective:To investigate the effects of Ganjiang granule(GG)on cecal microflora and serum biochemical components in rats with constipation-predominant irritable bowel syndrome(IBSeC).Methods:Twenty-four SpragueeDawley rats were randomly divided into four groups:control,model,GG,and probiotics.Rats in the model,GG,and probiotics groups received 3℃ tap water intragastrically;rats in the GG group were treated with GG;rats in the probiotics group were treated with probiotics.For all rats,enzyme-linked immunosorbent assay and colorimetry were used to assess serum biochemical components related to gastrointestinal function;16S rRNA high-throughput sequencing was used to analyze the cecal microflora.Results:The serum level of 5-hydroxytryptamine(HT)was higher in the model group than in the control group(Z=-2.082,P=.037).The model group exhibited changes in cecal microflora:the relative abundances of Lactobacillus decreased(Z=-2.882,P=.004)and Dorea increased(t=-3.030,P=.023),compared with the control group.The GG and probiotics groups exhibited normal serum levels of 5-HT.The GG and probiotics groups exhibited improved serum levels of gastrin;the probiotics group exhibited an improved serum level of vasoactive intestinal peptide.Compared with the model group,The GG group exhibited greater relative abundance of Ruminococcus(Z=-2.402,P=.016);the probiotics group exhibited greater relative abundance of SMB53(Z=-2.823,P=.005)and lower relative abundances of Desulfovibrio(Z=-2.823,P=.005)and Facklamia(Z=-2.608,P=.009).Conclusion:The effects of GG on IBS-C may be related to regulation of the serum level of 5-HT,as well as elevated relative abundance of beneficial bacteria in cecal microflora.

Characterization and phylogenetics of a new species of genus Lactobacillus from the activated sludge in biohydrogen production

Anaerobic process of biohydrogen production was developed. There is a great deal of Lactobacillus bacteria in the activated sludge of biohydrogen reactor. The isolation and identification of different anaerobic bacteria in the reactor is important for fermented biohydrogen production process by anaerobic digesting organic wastewater. Considering with the physiological and biochemical traits,morphological characteristics and 16SrDNA sequence,the isolated Rennanqilyf13 is a new species in Lactobacillus genus. And the temporary nomenclature of the species is Lactobacillus Strain Rennanqilyf13 sp. nov.

Changes of Intestinal Microecology in Patients with Primary Sjogren’s Syndrome after Therapy of Yangyin Yiqi Huoxue Recipe(养阴益气活血方)

Objective: To explore the change of intestinal microecology in patients with primary Sjogren’s syndrome(p SS) and correlation with disease activity, and also discuss the therapy effect of Yangyin Yiqi Huoxue Recipe(养阴益气活血方, YYHD). Methods: Sixteen p SS patients were enrolled in the present study, who received 3-month treatment of YYHR, 200 mL orally twice daily. Their pre-and post-test ESSDAI scores, erythrocyte sedimentation rate(ESR) and serum immunoglobulin G(IgG) levels were measured respectively. The 16 Sr DNA metagenomic sequencing was used to detect and analyze the abundance and diversity of intestinal bacteria flora and the proportion of bacteria at the levels of phylum, family, and genus, in comparision with those of 6 healthy subjects in the control group. Results: The abundance and diversity of intestinal bacteria flora in pSS patients were lower than those of healthy subjects(P<0.05). After the treatment with YYHD, patients’ ESSDAI score and levels of IgG and ESR have decreased significantly(P<0.05). At the phylum level, the proportions of Actinobacteria, Firmicutes, Fusobacteria and Proteobacteria have reduced sharply, while the proportions of Bacteroidetes, Teneriquetes and Candidate-division-TM7 have increased significantly by treatment(all P<0.05). At the classification level, such treatment has caused a significant decrease in the proportions of Bacteroidaceae, Ruminococcaceae, Veillonellaceae, and Enterobacteriacea(all P<0.05), but a significant increase in the proportion of Lachnospiraceae(P<0.05). At the genus level, the treatment has significantly decreased the proportions of Bifidobacterium, Bacteroides, Escherichia-Shigella, Faecalibacterium and Prevotella(all P<0.05), but significantly increased the proportion of Clostridia(P<0.05), close to the levels of healthy subjects(P>0.05). Conclusions: There exists an imbalance of intestinal microecology in p SS patients, which can be improved through the treatment with YYHD. Besides, such treatment can also improve the disease activity and adjust the diversity of intestinal bacteria flora, the composition and the abundance of intestinal flora.

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity

A number of basic and applied questions in ecology and environmental management require the characterization of soil and leaf litter faunal diversity. Recent advances in high-throughput sequencing of barcode-gene amplicons ('metabarcoding') have made it possible to survey biodiversity in a robust and efficient way. However, one obstacle to the widespread adoption of this technique is the need to choose amongst many candidates for bioinformatic processing of the raw sequencing data. We compare three candidate pipelines for the processing of 18S small subunit rDNA metabarcode data from solid substrates: (i) USEARCH/CROP, (ii) Denoiser/UCLUST, and (iii) OCTUPUS. The three pipelines produced reassuringly similar and highly correlated assessments of community composition that are dominated by taxa known to characterize the sampled environments. However, OCTUPUS appears to inflate phylogenetic diversity, because of higher sequence noise. We therefore recommend either the USEARCH/CROP or Denoiser/UCLUST pipelines, both of which can be run within the QIIME (Quantitative Insights Into Microbial Ecology) environment.

The intestinal microbiome of an Indo-Pacific humpback dolphin(Sousa chinensis)stranded near the Pearl River Estuary,China

The mammalian intestinal microbiome is critical for host health and disease resistance.However,the cetacean intestinal microbiota remains relatively unexplored.By using high-throughput 16S rRNA gene sequencing,we analyzed intestinal bacterial samples from an Indo-pacific humpback dolphin(Sousa chinensis)stranded near the Pearl River Estuary in China.The samples included 3 anatomical regions(foregut,midgut,and rectum)and 2 anatomical locations(content and mucus).Our analyses revealed that the dolphin intestinal bacteria contained 139 operational taxonomic units(OTUs),dominated at the phyla level by Firmicutes(47.05%in the content;94.77%in the mucus),followed by Bacteroidetes(23.63%in the content;1.58%in the mucus)and Gammaproteobacteria(14.82%in the content;2.05%in the mucus).The intestinal bacteria had a small core community(15 OTUs,accounting for 99.74%of the reads),some of which could be potentially pathogenic to both human and dolphins.As an alternative to sampling the dolphin intestinal bacteria,fecal sampling could be used.Additionally,function potentials such as,xenobiotics biodegradation,beta-lactam resistance,and human disease-related pathways,were detected in the dolphin intestinal bacteria.These findings provide the first baseline knowledge of the intestinal microbiome of the Indo-Pacific humpback dolphin,which may offer new insights into cetacean conservation by using microbial surveillance.

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.

Analysis of the microbial communities in soils of different ages following volcanic eruptions

Volcanism is a primary process of land formation.It provides a model for understanding soil-forming processes and the role of pioneer bacteria and/or archaea as early colonizers in those new environments.The objective of this study was to identify the microbial communities involved in soil formation.DNA was extracted from soil samples from the Llaima volcano in Chile at sites destroyed by lava in different centuries(1640,1751,and 1957).Bacterial and archaeal 16 S r RNA genes were analyzed using quantitative polymerase chain reaction(q PCR)and Illumina Mi Seq sequencing.Results showed that microbial diversity increased with soil age,particularly between the 1751 and 1640 soils.For archaeal communities,Thaumarchaeota was detected in similar abundances in all soils,but Euryarchaeota was rare in the older soils.The analysis of bacterial 16 S r RNA genes showed high abundances of Chloroflexi(37%),Planctomycetes(18%),and Verrucomicrobia(10%)in the youngest soil.Proteobacteria and Acidobacteria were highly abundant in the older soils(16%in 1640 and 15%in 1751 for Acidobacteria;38%in 1640 and 27%in 1751 for Proteobacteria).The microbial profiles in the youngest soils were unusual,with a high abundance of bacteria belonging to the order Ktedonobacterales(Chloroflexi)in the 1957 soil(37%)compared with the 1751(18%)and 1640(7%)soils.In this study,we show that there is a gradual establishment of the microbial community in volcanic soils following an eruption and that specific microbial groups can colonize during the early stages of recovery.