Microbiomes of Top and Sub-Layers of Semi-Arid Soils in North-Eastern Nigeria Are Rich in Firmicutes and Proteobacteria with Surprisingly High Diversity of Rare Species

Borno state is the second largest state in Nigeria with over 70,000 square kilometers of diverse ecosystems including parts of the fertile Lake Chad basin. However, more than 2/3 of this landmass is threatened with drought, advancing desertification and degraded soils. Most restoration efforts involve revegetation, which in the past has met with limited success. Microbial communities of soils play a pivotal role in soil fertility and plant cover. We conducted the first metagenomic amplicon sequencing study, comparing two soil depths to determine whether soil bacteria abundance and diversity in the harsh bare soils were sufficient to sustain greening efforts. The goal was to glean insights to guide microbial inoculant formulation needed in the region. Samples from top (0 - 15 cm) and sub (16 - 65 cm) soils were collected from five strategic locations in the state. Using next generation Illumina sequencing protocols, total DNA extracted directly from the soils was sequenced and analyzed by QIIME. Metadata collected from site showed scorching temperatures of over 46?C, near zero moisture level and a pH of about 6 for top soil. At 65 cm depth, the temperature averaged 32?C with a pH of 5 and significantly higher soil moisture of 0.1%. The bacterial community structure was unexpectedly very diverse at both soil depths samples, recording a ChaO1 index ranging from 909 to 4296 and a Shannon diversity range of 3.54 to 6.33. The most abundant phyla in both soil depths were the Firmicutes and Proteobacteria;however the relative abundance of composite lower taxa was strikingly different. Operational taxonomic units and diversity indices were highest for top soils and were dominated by members of resilient groups of Actinobacteria, Firmucutes, Acidobacteria and numerous other less well-known taxa whose individual relative abundance did not exceed 3% of total population. The high diversity and richness of Proteobacteria (at 65 cm depth), some of which are key to soil fertility, suggest that revegetation efforts could be improved by shifting the gradient of these microbiota upwards using shades and micro-irrigation. Soils in semi-arid regions in Nigeria contain numerous operational taxonomic bacterial groups with potential thermophilic and drought genetic resources to be mined. Microbial community structure beneath the top soil appears stable and should be the target sample for the assessments of climatic change impact on microbial community structure in environments like this.

肠道微生物与糖尿病关系的研究进展

深入研究人类共生微生物与糖尿病（Diabetes mellitus,DM）的关系,将为糖尿病的预防和治疗提供新的手段。越来越多的研究表明,肠道微生物在人类的健康和疾病中有极其重要的作用,它主要参与了疾病的发生发展过程。肠道微生物结构功能紊乱,会引发一系列的相关疾病,主要表现在代谢性疾病及免疫系统疾病方面。目前肠道微生物已被认为是治疗代谢性疾病的关键。本文就肠道微生物与糖尿病的相互关系作相关综述。

Modulation of faecal metagenome in Crohn's disease:Role of microRNAs as biomarkers

BACKGROUND The gut microbiota plays a key role in the maintenance of intestinal homeostasis and the development and activation of the host immune system. It has been shown that commensal bacterial species can regulate the expression of host genes. 16 S rRNA gene sequencing has shown that the microbiota in inflammatory bowel disease(IBD) is abnormal and characterized by reduced diversity. Micro RNAs(miRNAs) have been explored as biomarkers and therapeutic targets, since they are able to regulate specific genes associated with Crohn's disease(CD). In this work, we aim to investigate the composition of gut microbiota of active treatment-na?ve adult CD patients, with miRNA profile from gut microbiota.AIM To investigate the composition of gut microbiota of active treatment-na?ve adult CD patients, with miRNA profile from gut microbiota.METHODS Patients attending the outpatient clinics at Valme University Hospital without relevant co-morbidities were matched according to age and gender. Faecal samples of newonset CD patients, free of treatment, and healthy controls were collected. Faecal samples were homogenized, and DNA was amplified by PCR using primers directed to the 16 S bacterial rRNA gene. Pyrosequencing was performed using GS-Junior platform. For sequence analysis, MGRAST server with the database Ribosomal Project was used. MiRNA profile and their relative abundance were analyzed by quantitative PCR.RESULTS Microbial community was characterized using 16 S rRNA gene sequencing in 29 samples(n = 13 CD patients, and n = 16 healthy controls). The mean Shannon diversity was higher in the healthy control population compared to CD group(5.5 vs 3.7). A reduction in Firmicutes and an increase in Bacteroidetes were found. Clostridia class was also significantly reduced in CD. Principal components analysis showed a grouping pattern, identified in most of the subjects in both groups, showing a marked difference between control and CD groups. A functional metabolic study showed that a lower metabolism of carbohydrates(P = 0.000) was found in CD group, while the metabolism of lipids was increased. In CD patients, three miRNAs were induced in affected mucosa: mir-144(6.2 ± 1.3 fold), mir-519(21.8 ± 3.1) and mir-211(2.3 ± 0.4). CONCLUSION Changes in microbial function in active non-treated CD subjects and three miRNAs in affected vs non-affected mucosa have been found. miRNAs profile may serve as a biomarker.

Maternal sleep deprivation induces gut microbial dysbiosis and neuroinflammation in offspring rats

Maternal sleep deprivation(MSD)is a global public health problem that affects the physical and mental development of pregnant women and their newborns.The latest research suggests that sleep deprivation(SD)disrupts the gut microbiota,leading to neuroinflammation and psychological disturbances.However,it is unclear whether MSD affects the establishment of gut microbiota and neuroinflammation in the newborns.In the present study,MSD was performed on pregnant SpragueDawley rats in the third trimester of pregnancy(gestational days 15-21),after which intestinal contents and brain tissues were collected from offspring at different postnatal days(P1,P7,P14,and P56).Based on microbial profiling,microbial diversity and richness increased in pregnant rats subjected to MSD,as reflected by the significant increase in the phylum Firmicutes.In addition,microbial dysbiosis marked by abundant Firmicutes bacteria was observed in the MSD offspring.Furthermore,quantitative real-time polymerase chain reaction(q RT-PCR)and enzyme-linked immunosorbent assay(ELISA)showed that the expression levels of proinflammatory cytokines interleukin 1β(IL-1β)and tumor necrosis factorα(TNF-α)were significantly higher in the MSD offspring at adulthood(P56)than in the control group.Through Spearman correlation analysis,IL-1βand TNF-αwere also shown to be positively correlated with Ruminococcus_1 and Ruminococcaceae_UCG-005 at P56,which may determine the microbiota-host interactions in MSDrelated neuroinflammation.Collectively,these results indicate that MSD changes maternal gut microbiota and affects the establishment of neonatal gut microbiota,leading to neuroinflammation in MSD offspring.Therefore,understanding the role of gut microbiota during physiological development may provide potential interventions for cognitive dysfunction in MSD-impacted offspring.

Gut microbiome composition can predict the response to nivolumab in advanced hepatocellular carcinoma patients

BACKGROUND Immunotherapy has revolutionized the clinical outcomes of intractable cancer patients.Little is known about the intestinal nonpathogenic bacterial composition of hepatocellular carcinoma(HCC)patients treated by immunotherapy.AIM To determine whether there is a correlation between gut bacterial composition and prognosis in HCC patients.METHODS From September 2019 to March 2020,we prospectively collected fecal samples and examined the gut microbiome of 8 advanced HCC patients treated with nivolumab as a second-or third-line systemic treatment.Fecal samples were collected before the start of immunotherapy.Fecal samples of patients with progression during treatment were collected at the time of progression,and fecal samples of patients who showed good response to nivolumab were collected after 5-7 mo as follow-up.Metagenomic data from 16S ribosomal RNA sequencing were analyzed using CLC Genomics Workbench.Microbiome data were analyzed according to therapeutic response.RESULTS All 8 patients were male,of which 6 had underlying chronic hepatitis B.A higher Shannon index was found in the responders than in the non-responders after nivolumab therapy(P=0.036).The unweighted beta diversity analysis also showed that the overall bacterial community structure and phylogenetic diversity were clearly distinguished according to therapeutic response.There was no significant difference in the diversity or composition of the patient gut microbiome according to the immunotherapy used.Several taxa specific to therapeutic response were designated as follows:Dialister pneumosintes,Escherichia coli,Lactobacillus reteri,Streptococcus mutans,Enterococcus faecium,Streptococcus gordonii,Veillonella atypica,Granulicatella sp.,and Trchuris trichiura for the nonresponders;Citrobacter freundii,Azospirillum sp.and Enterococcus durans for the responders.Of note,a skewed Firmicutes/Bacteroidetes ratio and a low Prevotella/Bacteroides ratio can serve as predictive markers of non-response,whereas the presence of Akkermansia species predicts a good response.CONCLUSION The current presumptive study suggests a potential role for the gut microbiome as a prognostic marker for the response to nivolumab in treatment of HCC patients.

Characteristics of gut microbiota in representative mice strains:Implications for biological research

Background:Experimental animals are used to study physiological phenomena,pathological mechanisms,and disease prevention.The gut microbiome is known as a potential confounding factor for inconsistent data from preclinical studies.Although many gut microbiome studies have been conducted in recent decades,few have focused on gut microbiota fluctuation among representative mouse strains.Methods:A range of frequently used mouse strains were selected from 34 isolation packages representing disease-related animal(DRA),immunity defect animal(IDA),or gene-editing animal(GEA)from the BALB/c and C57BL/6J backgrounds together with normal mice,and their microbial genomic DNA were isolated from mouse feces to sequence for the exploration of gut microbiota.Results:Mouse background strain,classification,introduced source,introduced year,and reproduction type significantly affected the gut microbiota structure(p<0.001 for all parameters),with background strain contributing the greatest influence(R^(2)=0.237).In normal groups,distinct gut microbiota types existed in different mouse strains.Sixty-four core operational taxonomic units were obtained from normal mice,and 12 belonged to Lactobacillus.Interestingly,the gut microbiota in C57BL/6J was more stable than that in BALB/c mice.Furthermore,the gut microbiota in the IDA,GEA,and DRA groups significantly differed from that in normal groups(p<0.001 for all).Compared with the normal group,there was a significantly higher Chao 1 and Shannon index(p<0.001 for all)in the IDA,GEA,and DRA groups.Markedly changed classes occurred with Firmicutes and Bacteroidetes.The abundances of Helicobacter,Blautia,Enterobacter,Bacillus,Clostridioides,Paenibacillus,and Clostridiales all significantly decreased in the IDA,GEA,and DRA groups,whereas those of Saccharimonas,Rikenella,and Odoribacter all significantly increased.

Electro-acupuncture promotes gut motility and alleviates functional constipation by regulating gut microbiota and increasing butyric acid generation in mice

Objective:Abnormalities in the gut microbiota and intestinal short-chain fatty acid(SCFA)levels are implicated in the pathogenesis of functional constipation(FC).Electro-acupuncture(EA)has been shown to improve constipation-related symptoms and rebalance the gut microbiota.However,it is currently unknown whether the gut microbiota is a key mechanistic target for EA or how EA promotes gut motility by regulating the gut microbiota and SCFAs.Therefore,we assessed the effects of EA in FC mice and pseudo-germfree(PGF)mice to address these questions.Methods:Forty female Kunming mice were randomly separated into a normal control group(n=8),an FC group(n=8),an FC+EA group(n=8),a PGF group(n=8)and a PGF+EA group(n=8).The FC group and FC+EA group were treated with diphenoxylate to establish the FC model;the PGF group and PGF+EA group were given an antibiotic cocktail to initiate the PGF model.After maintaining the model for 14 d,mice in the FC+EA and PGF+EA groups received EA stimulation at the ST25 and ST37 acupoints,once a day,5 times per week,for 2 weeks.Fecal parameters and intestinal transit rate were calculated to assess the efficacy of EA on constipation and gastrointestinal motility.Colonic contents were used to quantify gut microbial diversity using 16S rRNA sequencing,and measure SCFA concentrations using gas chromatography-mass spectrometry.Results:EA significantly shortened the first black stool defecation time(P<0.05)and increased the intestinal transit rate(P<0.01),and fecal pellet number(P<0.05),wet weight(P<0.05)and water content(P<0.01)over 8 h,compared with the FC group,showing that EA promoted gut motility and alleviated constipation.However,EA treatment did not reverse slow-transit colonic motility in PGF mice(P>0.05),demonstrating that the gut microbiota may play a mechanistic role in the EA treatment of constipation.In addition,EA treatment restored the Firmicutes to Bacteroidetes ratio and significantly increased butyric acid generation in FC mice(P<0.05),most likely due to the upregulation of Staphylococcaceae microorganisms(P<0.01).Conclusion:EA-mediated resolution of constipation occurs through rebalancing the gut microbiota and promoting butyric acid generation.

The temporal fluctuations and development of faecal microbiota in commercial layer flocks

The microbiota of the gastrointestinal tract influences gut health,which in turn strongly impacts the general health and productivity of laying hens.It is essential to characterise the composition and temporal development of the gut microbiota in healthy layers raised under different management systems,to understand the variations in typical healthy microbiota structure,so that deviations from this might be recognised and correlated with production and health issues when they arise.The present investigation aimed to study the temporal development and phylogenetic composition of the gut microbiota of four commercially raised layer flocks from hatch to end of the production cycle.Non-intrusive faecal sampling was undertaken as a proxy to represent the gut microbiota.Sequencing of 16S rRNA gene amplicons was used to characterise the microbiota.Beta diversity analysis indicated that each faecal microbiota was different across the four flocks and had subtly different temporal development patterns.Despite these inter-flock differences,common patterns of microbiota development were identified.Firmicutes and Proteobacteria were dominant at an early age in all flocks.The microbiota developed gradually during the rearing phase;richness and diversity increased after 42 d of age and then underwent significant changes in composition after the shift to the production farms,with Bacteroidota becoming more dominant in older birds.By developing a more profound knowledge of normal microbiota development in layers,opportunities to harness the microbiota to aid in the management of layer gut health and productivity may be more clearly seen and realised.

Exercise and gut microbiota: clinical implications for the feasibility of Tai Chi

Recent studies have shown exercise is associated with changes in the gut microbiota in humans as well as in experimental animals. Tai Chi is an exercise that integrates a martial art, deep breathing and mediation, and has various beneficial effects for health. This review summarizes current knowledge and recent literature on the association between exercise and gut microbiota, and explores the feasibility of Tai Chi for improving gut microbiota composition and function. PubMed/MEDLINE was used to search the English literature for the keywords exercise and gut microbiota. Fourteen relevant studies were identified. In humans, exercise increases the gut microbial diversity. However, the evidence for this association is weak, as previous studies were small-scale, non-controlled studies of short duration or cross-sectional design. In animals, exercise alters the composition of gut microbiota, with some studies suggesting exercise increases the Bacteroidetes/ Firmicutes ratio. However, these results are controversial, partly because host genetics and physical fitness also influence gut microbiota. Furthermore, the intensity of exercise may play a key role in how exercise affects gut microbiota. Tai Chi is a moderate-intensity exercise that improves immune function and inflammation of the gut. Tai Chi may also affect gut microbiota through vagal modulation and mediating the hypothalamic-pituitary-adrenal axis. However, no studies have investigated the association between Tai Chi and gut microbiota. Well designed studies exploring the effects of Tai Chi on gut microbiota are needed.

Impact of disinfection on drinking water biofilm bacterial community

Disinfectants are commonly applied to control the growth of microorganisms in drinking water distribution systems. However, the effect of disinfection on drinking water microbial community remains poorly understood. The present study investigated the impacts of different disinfectants（chlorine and chloramine） and dosages on biofilm bacterial community in bench-scale pipe section reactors. Illumina MiS eq sequencing illustrated that disinfection strategy could affect both bacterial diversity and community structure of drinking water biofilm. Proteobacteria tended to predominate in chloraminated drinking water biofilms, while Firmicutes in chlorinated and unchlorinated biofilms. The major proteobacterial groups were influenced by both disinfectant type and dosage. In addition, chloramination had a more profound impact on bacterial community than chlorination.

Culturable aerobic and facultative bacteria from the gut of the polyphagic dung beetle Thorectes lusitanicus

Unlike other dung beetles, the Iberian geotrupid, Thorectes lusitanicus, exhibits polyphagous behavior; for example, it is able to eat acorns, fungi, fruits, and carrion in addition to the dung of different mammals. This adaptation to digest a wider diet has physiological and developmental advantages and requires key changes in the composition and diversity of the beetle＇s gut microbiota. In this study, we isolated aerobic, facultative anaerobic, and aerotolerant microbiota amenable to grow in culture from the gut contents of T. lusitanicus and resolved isolate identity to the species level by sequencing 16S rRNA gene fragments. Using BLAST similarity searches and maximum likelihood phylogenetic analyses, we were able to reveal that the analyzed fraction （culturable, aerobic, facultative anaerobic, and aerotolerant） of beetle gut microbiota is dominated by the phyla Pro- teobacteria, Firmicutes, and Actinobacteria. Among Proteobacteria, members of the order Enterobacteriales （Gammaproteobacteria） were the most abundant. The main functions associated with the bacteria found in the gut of T. lusitanicus would likely include nitrogen fixation, denitrification, detoxification, and diverse defensive roles against pathogens.

Intestinal microecology in rats with ulcerative colitis

Objective To study the abundance and diversity ofthe gut flora in rats with dextran sulfate sodium(DSS)-induced ulcerative colitis(UC)to provide new knowledge about the pathogenesis of this disease.Methods