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.

Identification of Bacterial Fish Pathogens in Brazil by Direct Colony PCR and 16S rRNA Gene Sequencing

Intensive fish farming systems in Brazil have increased the disease incidence, mainly of bacterial origin, due to higher stocking density, high organic matter levels and poor quality of the aquatic environment that causes high mortality rates during outbreaks. The identification of pathogenic species using a fast and reliable method of diagnosis is essential for successful epidemiological studies and disease control. The present study evaluated the use of direct colony PCR in combination with 16S rRNA gene sequencing to diagnose fish bacterial diseases, with the goal of reducing the costs and time necessary for bacterial identification. The method was successful for all 178 isolates tested and produced bands with the same intensity as the standard PCR performed using pure DNA. In conclusion, the genetics methods allowed detecting the most common and important pathogens in Aquaculture, including 12 species of occurrence in Brazilian fish farms. The results of the present study constitute an advance in the available diagnostic methods for bacterial pathogens in fish farms.

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.

Enterococcus faecalis provides protection during scavenging in carrion crow (Corvus corone)

The gut microbiota significantly influences host physiology and provides essential ecosystem services.While diet can affect the composition of the gut microbiota,the gut microbiota can also help the host adapt to specific dietary habits.The carrion crow(Corvus corone),an urban facultative scavenger bird,hosts an abundance of pathogens due to its scavenging behavior.Despite this,carrion crows infrequently exhibit illness,a phenomenon related to their unique physiological adaptability.At present,however,the role of the gut microbiota remains incompletely understood.In this study,we performed a comparative analysis using 16S rRNA amplicon sequencing technology to assess colonic content in carrion crows and 16 other bird species with different diets in Beijing,China.Our findings revealed that the dominant gut microbiota in carrion crows was primarily composed of Proteobacteria(75.51%)and Firmicutes(22.37%).Significant differences were observed in the relative abundance of Enterococcus faecalis among groups,highlighting its potential as a biomarker of facultative scavenging behavior in carrion crows.Subsequently,E.faecalis isolated from carrion crows was transplanted into model mice to explore the protective effects of this bacterial community against Salmonella enterica infection.Results showed that E.faecalis down-regulated the expression of pro-inflammatory cytokines tumor necrosis factor alpha(TNF-α),interferon gamma(IFN-γ),and interleukin 6(IL-6),prevented S.enterica colonization,and regulated the composition of gut microbiota in mice,thereby modulating the host’s immune regulatory capacity.Therefore,E.faecalis exerts immunoregulatory and anti-pathogenic functions in carrion crows engaged in scavenging behavior,offering a representative case of how the gut microbiota contributes to the protection of hosts with specialized diets.

Intratumoural microorganism can affect the progression of hepatocellular carcinoma

BACKGROUND Several recent studies have confirmed that intratumoural microorganisms can affect the occurrence and development of hepatocellular carcinoma(HCC);however,their role in tumor progression remains unclear.Hence,there is a need for further research on the role of intratumoural microorganisms in HCC.AIM To investigate the changes in intratumoural microorganisms in HCC and the effect of Propionibacterium on HCC progression.METHODS HCC and normal liver tissue specimens were subjected to fluorescence in situ hybridization(FISH).After performing 16S rRNA sequencing on HCC and peritumoral tissues to analyze the differences between the two groups.Propionibacterium was cocultured with HCC cells in vitro.Changes in cell proliferation and migration capacity were evaluated.The expression of NF-κB pathway related proteins in tumor cells was compared.The orthotopic liver implantation model and the subcutaneous xenograft model were constructed.liver tissues and subcutaneous tumors were collected 2 weeks later.RESULTS FISH demonstrated the presence of microorganisms in HCC and normal liver tissues.16S rRNA sequencing revealed an abundance of Lysobacter,Lachnospiraceae,Pseudomonas,and Lactobacillus in HCC tissues.The distribution and abundance of Propionibacterium showed differences between HCC and peritumoral tissues(P<0.05).In vitro studies demonstrated that Propionibacterium and its metabolite propionic acid(PA)inhibited the proliferation and migration of HCC cells(P<0.05).The expression of the proteins in NF-κB signaling pathway also decreased in HCC cells(P<0.05).CONCLUSION Microorganisms in HCC and normal liver tissues displayed significant disparities.The PA-producing bacterium Propionibacterium in HCC exerts an effect on the NF-κB pathway,thereby affecting the biological behavior of HCC.

Relationship between hyperlipidemia and the gut microbiome of rats, characterized using high-throughput sequencing

Objective:To determine the effects of a high-fat diet(HFD)on the gut microbiome in rats,to explore the relationship between the intestinal flora and blood lipid profile.Methods:SpragueeDawley rats were fed an HFD for four weeks to induce hyperlipidemia,then 16S rRNA sequencing was used to compare the intestinal flora between hyperlipidemic and control diet-fed rats.Results:The microbiome of rats fed an HFD for four weeks differed from that of control diet-fed rats.Bacterial species that were less abundant were most affected by HFD feeding,among which were many pathogenic species,which became significantly more abundant.Eighteen genera were present in significantly different numbers in hyperlipidemic and control rats,more than half of which have been linked to infection and inflammation,or energy intake and obesity.The results indicated a type of stress response of the flora to a high-fat environment.In addition,the age of the rats tended to influence the gut microbial composition.Conclusion:These findings suggest that HFD may induce hyperlipidemia by affecting the gut microbial composition.Changes in the abundance of pro-inflammatory and pathogenic bacteria,and those that influence energy intake and obesity,may be important mediators of this.

Determining the protective effects of Ma-Mu-Ran Antidiarrheal Capsules against acute DSS-induced enteritis using 16S rRNA gene sequencing and fecal metabolomics

Ma-Mu-Ran Antidiarrheal Capsules(MMRAC)is traditional Chinese medicine that has been used to treat diarrhea caused by acute enteritis(AE)and bacillary dysentery in Xinjiang(China)for many years.However,the potential therapeutic mechanism of MMRAC for AE and its regulatory mechanism on host metabolism is unclear.This study used fecal metabolomics profiling with GC/MS and 16S rRNA gene sequencing analysis to explore the potential regulatory mechanisms of MMRAC on a dextran sulfate sodium salt(DSS)-induced mouse model of AE.Fecal metabolomics-based analyses were performed to detect the differentially expressed metabolites and metabolic pathways.The 16S rRNA gene sequencing analysis was used to assess the altered gut microbes at the genus level and for functional prediction.Moreover,Pearson correlation analysis was used to integrate differentially expressed metabolites and altered bacterial genera.The results revealed that six intestinal bacteria and seven metabolites mediated metabolic disorders(i.e.,metabolism of amino acid,carbohydrate,cofactors and vitamins,and lipid)in AE mice.Besides,ten altered microbes mediated the differential expression of eight metabolites and regulated these metabolisms after MMRAC administration.Overall,these findings demonstrate that AE is associated with metabolic disorders and microbial dysbiosis.Further,we present that MMRAC exerts protective effects against AE by improving host metabolism through the intestinal flora.

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.

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 the human oral microbiome in cholangiocarcinoma

Dear Editor,Alterations in the human microbiome are closely related to various hepatobiliary diseases.Gut microbial dysbiosis has been found in patients with cholangiocarcinoma(CCA)[1].However,the characteristics of oral microbiome in patients with CCA have not been studied.

Changes in the gut microbiota of osteoporosis patients based on 16S rRNA gene sequencing:a systematic review and meta-analysis

Background:Osteoporosis(OP)has become a major public health issue,threatening the bone health of middle-aged and elderly people from all around the world.Changes in the gut microbiota(GM)are correlated with the maintenance of bone mass and bone quality.However,research results in this field remain highly controversial,and no systematic review or meta-analysis of the relationship between GM and OP has been conducted.This paper addresses this shortcoming,focusing on the difference in the GM abundance between OP patients and healthy controls based on previous 16S ribosomal RNA(rRNA)gene sequencing results,in order to provide new clinical reference information for future customized prevention and treatment options of OP.Methods:According to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses(PRISMA),we comprehensively searched the databases of Pub Med,Web of Science,Embase,Cochrane Library,and China National Knowledge Infrastructure(CNKI).In addition,we applied the R programming language version 4.0.3 and Stata 15.1 software for data analysis.We also implemented the Newcastle-Ottawa Scale(NOS),funnel plot analysis,sensitivity analysis,Egger’s test,and Begg’s test to assess the risk of bias.Results:This research ultimately considered 12 studies,which included the fecal GM data of 2033 people(604 with OP and 1429 healthy controls).In the included research papers,it was observed that the relative abundance of Lactobacillus and Ruminococcus increased in the OP group,while the relative abundance for Bacteroides of Bacteroidetes increased(except for Ireland).Meanwhile,Firmicutes,Blautia,Alistipes,Megamonas,and Anaerostipes showed reduced relative abundance in Chinese studies.In the linear discriminant analysis Effect Size(LEfSe)analysis,certain bacteria showed statistically significant results consistently across different studies.Conclusions:This observational meta-analysis revealed that changes in the GM were correlated with OP,and variations in some advantageous GM might involve regional differences.

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.

Gut mucosal microbiota profiles linked to colorectal cancer recurrence

BACKGROUND Emerging evidence links gut microbiota to various human diseases including colorectal cancer(CRC)initiation and development.However,gut microbiota profiles associated with CRC recurrence and patient prognosis are not completely understood yet,especially in a Chinese cohort.AIM To investigate the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis.METHODS We obtained the composition and structure of gut microbiota collected from 75 patients diagnosed with CRC and 26 healthy controls.The patients were followed up by regular examination to determine whether tumors recurred.Triplet-paired samples from on-tumor,adjacent-tumor and off-tumor sites of patients diagnosed with/without CRC recurrence were analyzed to assess spatial-specific patterns of gut mucosal microbiota by 16S ribosomal RNA sequencing.Next,we carried out bioinformatic analyses,Kaplan-Meier survival analyses and Cox regression analyses to determine the relationship between gut mucosal microbiota profiles and CRC recurrence and patient prognosis.RESULTS We observed spatial-specific patterns of gut mucosal microbiota profiles linked to CRC recurrence and patient prognosis.A total of 17 bacterial genera/families were identified as potential biomarkers for CRC recurrence and patient prognosis,including Anaerotruncus,Bacteroidales,Coriobacteriaceae,Dialister,Eubacterium,Fusobacterium,Filifactor,Gemella,Haemophilus,Mogibacteriazeae,Pyramidobacter,Parvimonas,Porphyromonadaceae,Slackia,Schwartzia,TG5 and Treponema.CONCLUSION Our work suggests that intestinal microbiota can serve as biomarkers to predict the risk of CRC recurrence and patient death.

Salmonella Typhimurium infection disrupts but continuous feeding of Bacillus based probiotic restores gut microbiota in infected hens

Background:The gut microbiota plays an important role in the colonisation resistance and invasion of pathogens.Salmonella Typhimurium has the potential to establish a niche by displacing the microbiota in the chicken gut causing continuous faecal shedding that can result in contaminated eggs or egg products.In the current study,we investigated the dynamics of gut microbiota in laying chickens during Salmonella Typhimurium infection.The optimisation of the use of an infeed probiotic supplement for restoration of gut microbial balance and reduction of Salmonella Typhimurium load was also investigated.Results:Salmonella infection caused dysbiosis by decreasing(FDR<0.05)the abundance of microbial genera,such as Blautia,Enorma,Faecalibacterium,Shuttleworthia,Sellimonas,Intestinimonas and Subdoligranulum and increasing the abundance of genera such as Butyricicoccus,Erysipelatoclostridium,Oscillibacter and Flavonifractor.The higher Salmonella Typhimurium load resulted in lower(P<0.05)abundance of genera such as Lactobacillus,Alistipes,Bifidobacterium,Butyricimonas,Faecalibacterium and Romboutsia suggesting Salmonella driven gut microbiota dysbiosis.Higher Salmonella load led to increased abundance of genera such as Caproiciproducens,Acetanaerobacterium,Akkermansia,Erysipelatoclostridium,Eisenbergiella,EscherichiaShigella and Flavonifractor suggesting a positive interaction of these genera with Salmonella in the displaced gut microbiota.Probiotic supplementation improved the gut microbiota by balancing the abundance of most of the genera displaced by the Salmonella challenge with clearer effects observed with continuous supplementation of the probiotic.The levels of acetate and butyrate in the faeces were not affected(P>0.05)by Salmonella challenge and the butyrate level was increased by the continuous feeding of the probiotic.Probiotic supplementation in Salmonella challenged chickens resulted in higher level of propionate.Continuous probiotic supplementation decreased(P<0.05)the overall mean load of Salmonella in faeces and had a significant effect on Salmonella load reduction in internal organs.Conclusions:Salmonella challenge negatively impacts the diversity and abundance of many gut microbial genera involved in important functions such as organic acid and vitamin production.Strategic feeding of a Bacillus based probiotic helps in restoring many of the microbial genera displaced by Salmonella Typhimurium challenge.

Mucosa-associated bacteria in two middle-aged women diagnosed with collagenous colitis

AIM:To characterize the colon microbiota in two women histologically diagnosed with collagenous colitis using a culture-independent method.METHODS:Biopsies were taken from the ascending colon and the total DNA was extracted.Universal bacterial primers were used to amplify the bacterial 16S rRNA genes.The amplicons were then cloned into competent Escherichia coli cells.The clones were sequenced and identified by comparison to known sequences.RESULTS:The clones could be divided into 44 different phylotypes.The microbiota was dominated by Firmicutes and Bacteroidetes.Seven phylotypes werefound in both patients and constituted 47.5% of the total number of clones.Of these,the most dominating were clones similar to Bacteroides cellulosilyticus,Bacteroides caccae,Bacteroides thetaiotaomicron,Bacteroides uniformis and Bacteroides dorei within Bacteroidetes.Sequences similar to Faecalibacterium prausnitzii and Clostridium citroniae were also found in both patients.CONCLUSION:A predominance of potentially pathogenic Bacteroides spp.,and the presence of clones showing similarity to Clostridium clostridioforme were found but the overall colon microbiota showed similarities to a healthy one.Etiologies for collagenous colitis other than an adverse bacterial flora must also be considered.

Study on Tongue Coating Microbiota in Patients with Atrophic Gastritis

Aims: To explore the tongue coating microbiota composition in patients with atrophic gastritis by using the 16S rRNA gene sequencing technology. Methods: The study included 29 atrophic gastritis patients and 29 age and gender-matched non-atrophic gastritis controls. By sequencing the V3-V4 region of the 16S rRNA, we investigated the microbial community structure and diversity on the tongue coating. Results: There was no significant difference in the microbial diversity on the tongue coating between the two groups. However, compared with the control, the atrophic gastritis group had a smaller number of operational taxonomic units (OTUs). At the class level, patients with atrophic gastritis had lower relative abundances of Betaproteobacteria and Spirochaetia than the control group. At the gene level, the abundance of Neisseria and Aggregatibacter in atrophic gastritis group had significantly decreased compared with control ones. Furthermore, functional prediction revealed that 24 metabolic pathways significantly differed between the two groups. Conclusions: Our findings provide novel evidence that tongue coating microbiota may be a biomarker for characterizing patient with atrophic gastritis, but its mechanism needs to be further elaborated.

Scanning electron microscopy coupled with energydispersive X-ray spectrometry for quick detection of sulfuroxidizing bacteria in environmental water samples

Detection of sulfur-oxidizing bacteria has largely been dependent on targeted gene sequencing technology or traditional cell cultivation, which usually takes from days to months to carry out. This clearly does not meet the requirements of analysis for time-sensitive samples and/or complicated environmental samples. Since energy-dispersive X-ray spectrometry(EDS) can be used to simultaneously detect multiple elements in a sample, including sulfur, with minimal sample treatment, this technology was applied to detect sulfur-oxidizing bacteria using their high sulfur content within the cell. This article describes the application of scanning electron microscopy imaging coupled with EDS mapping for quick detection of sulfur oxidizers in contaminated environmental water samples, with minimal sample handling. Scanning electron microscopy imaging revealed the existence of dense granules within the bacterial cells, while EDS identified large amounts of sulfur within them. EDS mapping localized the sulfur to these granules. Subsequent 16S rRNA gene sequencing showed that the bacteria detected in our samples belonged to the genus Chromatium, which are sulfur oxidizers. Thus, EDS mapping made it possible to identify sulfur oxidizers in environmental samples based on localized sulfur within their cells, within a short time(within 24 h of sampling). This technique has wide ranging applications for detection of sulfur bacteria in environmental water samples.

Assessing the microbiota of recycled bedding sand on a Wisconsin dairy farm

Background:Sand is often considered the preferred bedding material for dairy cows as it is thought to have lower bacterial counts than organic bedding materials and cows bedded on sand experience fewer cases of lameness and disease.Sand can also be efficiently recycled and reused,making it cost-effective.However,some studies have suggested that the residual organic material present in recycled sand can serve as a reservoir for commensal and pathogenic bacteria,although no studies have yet characterized the total bacterial community composition.Here we sought to characterize the bacterial community composition of a Wisconsin dairy farm bedding sand recycling system and its dynamics across several stages of the recycling process during both summer and winter using 16S rRNA gene amplicon sequencing.Results:Bacterial community compositions of the sand recycling system differed by both seasons and stage.Summer samples had higher richness and distinct community compositions,relative to winter samples.In both summer and winter samples,the diversity of recycled sand decreased with time drying in the recycling room.Compositionally,summer sand 14 d post-recycling was enriched in operational taxonomic units(OTUs)belonging to the genera Acinetobacter and Pseudomonas,relative to freshly washed sand and sand from cow pens.In contrast,no OTUs were found to be enriched in winter sand.The sand recycling system contained an overall core microbiota of 141 OTUs representing 68.45%±10.33%SD of the total bacterial relative abundance at each sampled stage.The 4 most abundant genera in this core microbiota included Acinetobacter,Psychrobacter,Corynebacterium,and Pseudomonas.Acinetobacter was present in greater abundance in summer samples,whereas Psychrobacter and Corynebacterium had higher relative abundances in winter samples.Pseudomonas had consistent relative abundances across both seasons.Conclusions:These findings highlight the potential of recycled bedding sand as a bacterial reservoir that warrants further study.

Phenotypic and Genetic Characteristics of a Bordetella hinzii Isolated from a Rex Rabbit

A Bordetella hinzii strain, isolated from the lung of a dead breast-feeding infant rex rabbit with a respiratory infection, was used as study object to investigate its phenotypic and genetic characteristics. The strain could grow on MacConkey agar and was gram-negative, oxidase-positive, catalase-positive, short rodshaped, and it can produce alkali from malonate. Its 6S rRNA sequence was partially identical with B. hinzii （AF177667）. Animal experiments revealed nasal mucous hyperemia, tracheal congestion and bronchopneumonia in 28-day old rex rabbits. To sum up, this Bordetella hinzii isolate was deemed as a novel causative agent of respiratory disease in rex rabbit.

A Study of Prevalence and Pathogenic Activity of Bacteria in the Air of Dhaka City and Their Antimicrobial Resistance Pattern

Bangladesh composes the most polluted air with Dhaka securing the top position. The purpose of the study is the enumeration of the prevalence of pathogenic bacteria in Dhaka city’s air and their antibiotic susceptibility to the common antibiotics. For the sample collection, different selective media was exposed in air where the highest and lowest CFU was 137 and 1 respectively. Pathogens were screened through Hemolysis, DNase and Coagulase test and identified by 16s rRNA sequencing followed by antibiotic susceptibility test. 16s rRNA sequencing revealed that the organisms were Bacillus altitudinis strain 41KF2bT.28, Bacillus licheniformis strain QMA46-2, Bacillus altitudinis, Bacillus pumilis strain BJ-DEBCR-34, Staphylococcus aureus strain TPS3156, Bacillus sp CO16, Pseudomonas sp strain 96LC22 and Shigella dysenteriae strain ATCC 13313. Shigella dysenteriae, Staphylococcus aureus were 81.81% and 54.54% resistant to the antibiotics. Whole-genome sequencing would help to observe mutations in the traits as changes in hemolytic activity were found during pathogenecity tests.