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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

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Advances in Microbiology 2019年第1期9卷 102-118页

作者： Mwajim Bukar Oluwole Sodipo Karim Dawkins Roberto Ramirez Jummai T. Kaldapa Martha Tarfa Nwadiuto Esiobu North-East Zonal Biotechnology Centre of Excellence University of Maiduguri Maiduguri Nigeria Biochemistry Department Faculty of Science University of Maiduguri Maiduguri Nigeria Biological Sciences Department Microbial Biotech Laboratory Florida Atlantic University Boca Raton FL USA

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,

关键词： Microbiomes Semi-Arid Soils Microbial Community Structure Soil Bacteria Soil Fertility Top-Soil Re-Vegetation proteobacteria Firmicutes Sub-Surface OTU

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New insights into the interactions between the gut microbiota and the inflammatory response to ulcerative colitis in a mouse model of dextran sodium sulfate and possible mechanisms of action for treatment with PE&AFWE

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Animal Models and Experimental Medicine 2024年第2期7卷 83-97页

作者： Qianhui Fu Xiaoqin Ma Shuchun Li Mengni Shi Tianyuan Song Jian Cui Key Laboratory of Ethnomedicine of Ministry of Education School of PharmacyMinzu University of ChinaBeijingChina

Background:Inflammatory bowel disease(IBD),comprising Crohn's disease(CD)and ulcerative colitis(UC),is a heterogeneous state of chronic intestinal *** innate immunity,including innate immune cells,defends against pathogens and excessive entry of gut microbiota,while preserving immune tolerance to resident intestinal microbiota,and may be characterized by its capacity to produce a rapid and nonspecific *** association between microbiota dysbiosis and the pathogenesis of IBD is complex and *** the intestinal ecosystem is in dysbiosis,the reduced abundance and diversity of intestinal gut microbiota make the host more vulnerable to the attack of exogenous and endogenous pathogenic gut *** aim of our study was to comprehensively assess the relationship between microbial populations within UC,the signaling pathways of pathogenic gut microbe therein and the inflammatory response,as well as to understand the effects of using PE&AFWE(poppy extract[Papaver nudicaule L.]and Artemisia frigida ***)on UC ***:A UC mouse model was established by inducing SPF-grade C57BL/6 mice using dextrose sodium sulfate(DSS).Based on metagenomic sequencing to characterize the gut microbiome,the relationship between gut microbiota dysbiosis and gut microbiota was further studied using random forest and Bayesian network analysis methods,as well as histopathological ***:(1)We found that the 5 gut microbiota with the highest relative abundance of inflammatory bowel disease UC model gut microbiota were consistent with the top 5 ranked natural *** were three types of abundance changes in the model groups:increases(Chlamydiae/proteobacteria and Deferribacteres),decreases(Firmicutes),and no significant changes(Bacteroidetes).The UC model group was significantly different from the control group,with 1308 differentially expressed species with abundance changes greater than or equal to 2-fold.(2)The proportion

关键词： Arachidonic acid metabolism Gut microbiota Microbial dysbiosis proteobacteria

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Gut microbiota in preterm infants receiving breast milk or mixed feeding

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World Journal of Clinical Pediatrics 2024年第2期13卷 135-145页

作者： Sandra Gabriela Sánchez-González Bárbara Gabriela Cárdenas-del-Castillo Elvira Garza-González Gerardo R Padilla-Rivas Isaías Rodríguez-Balderrama Consuelo Treviño-Garza Fernando Félix Montes-Tapia Gerardo C Palacios-Saucedo Anthony Gutiérrez-Rodríguez Manuel Enrique de-la-O-Cavazos Department of Pediatrics Hospital Universitario“Dr.JoséEleuterio González”Universidad Autónoma de Nuevo LeónMonterrey 64460Nuevo LeónMéxico Departamento de Bioquímica y Medicina Molecular Universidad Autónoma de Nuevo LeónMonterrey 64460Nuevo LeónMéxico Department of Biochemistry and Molecular Medicine Universidad Autónoma de Nuevo LeónMonterrey 64460Nuevo LeónMéxico Department of Pediatric Surgery Hospital Universitario"Dr.JoséEleuterio González"Monterrey 64460Nuevo LeónMéxico

BACKGROUND Preterm birth is the leading cause of mortality in newborns,with very-low-birthweight infants usually experiencing several *** milk is considered the gold standard of nutrition,especially for preterm infants with delayed gut colonization,because it contains beneficial microorganisms,such as Lactobacilli and *** To analyze the gut microbiota of breastfed preterm infants with a birth weight of 1500 g or *** An observational study was performed on preterm infants with up to 36.6 wk of gestation and a birth weight of 1500 g or less,born at the University Hospital ***éEleuterio González at Monterrey,Mexico.A total of 40 preterm neonates were classified into breast milk feeding(BM)and mixed feeding(MF)groups(21 in the BM group and 19 in the MF group),from October 2017 to June *** samples were collected before they were introduced to any feeding *** full enteral feeding was achieved,the composition of the gut microbiota was analyzed using 16S rRNA gene *** variables were compared using Student’s t-test or using the Mann–Whitney U test for nonparametric ***,evenness,equitability,Margalef’s index,Fisher’s alpha,Chao-1 index,and Shannon’s diversity index were also *** No significant differences were observed at the genus level between the *** comparison indicated higher counts of Alphaproteobacteria and Betaproteobacteria in the initial compared to the final sample of the BM group(Pproteobacteria were detected in the final than in the initial sample(P=0.040).According to the Margalef index,Fisher’s alpha,and Chao-1 index,a decrease in species richness from the initial to the final sample,regardless of the feeding type,was observed(Pproteobacteria,with proteobacteria being the most ***,no significant differences were

关键词： Gut microbiota Human milk Preterm infant proteobacteria Very low birth weight 16S rRNA

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

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Animal Nutrition 2023年第4期15卷 197-209页

作者： Nitish Joat Yadav S.Bajagai Thi Thu Hao Van Dragana Stanley Kapil Chousalkar Robert J.Moore School of Animal and Veterinary Sciences The University of AdelaideRoseworthySouth Australia5371Australia Institute for Future Farming Systems Central Queensland UniversityRockhamptonQueensland4701Australia School of Science RMIT UniversityBundooraVictoria3083Australia

The microbiota of the gastrointestinal tract influences gut health,which in turn strongly impacts the general health and productivity of laying *** 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 *** 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 ***-intrusive faecal sampling was undertaken as a proxy to represent the gut *** of 16S rRNA gene amplicons was used to characterise the *** diversity analysis indicated that each faecal microbiota was different across the four flocks and had subtly different temporal development *** these inter-flock differences,common patterns of microbiota development were *** and proteobacteria were dominant at an early age in all *** 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 *** 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.

关键词： Chicken microbiota Faecal microbiota Firmicutes Housing condition proteobacteria

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Effects of dietary supplementation of bacteriophage cocktail on health status of weanling pigs in a non-sanitary environment

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Journal of Animal Science and Biotechnology 2023年第4期14卷 1661-1677页

作者： YoHan Choi Abdolreza Hosseindoust Sang Hun Ha Joeun Kim YeJin Min YongDae Jeong JunYoung Mun SooJin Sa JinSoo Kim Swine Science Division National Institute of Animal ScienceRural Development AdministrationCheonan 31000Republic of Korea Department of Animal Industry Convergence Kangwon National UniversityChuncheon 24341Republic of Korea

Background The study evaluated the effects of bacteriophage cocktail(BP)and ZnO administered during weaning time for piglets exposed to a non-sanitary *** bacteriophages were designed to eliminate Escherichia coli(K88,K99 and F41),Salmonella(typhimurium and enteritidis),and Clostridium perfreingens(types A and C).Forty 21-day-old crossbreed piglets were assigned to four treatments,including the PC(sanitary environment),NC(nonsanitary environment),BP(NC plus 108 pfu/kg BP),and ZO(NC plus 2,500 mg/kg ZnO).Piglets in the NC,BP and ZO were kept in a non-sanitary environment for 14 d,which was contaminated with the feces of infected *** Pigs in the BP and ZO treatments had a higher final body weight compared with the *** NC treatment showed the highest concentration of inflammatory cytokines including interleukin(IL)-1β,IL-6 and tumor necrosis factor-αin the *** administration of BP and ZO showed lower myeloperoxidase concentrations compared with the *** NC treatment showed a lower concentration of superoxide dismutase in serum compared with the *** the treatments in non-sanitary environment,the NC treatment showed a higher concentration of malondialdehyde compared with the *** PC treatment showed a lower concentration of butyric acid in the feces compared with the BP *** non-sanitary treatments,the villus height in the duodenum was greater in the BP and ZO compared with the *** lower abundance of proteobacteria phylum was observed in the BP and PC treatments compared with the *** highest relative abundance of Eubacterium was recorded in the BP *** abundance of Megasphaera and Schwartzia was higher in the NC pigs compared with the BP *** abundance of Desulfovibrio was lower in the supplemented treatments(BP and ZO)compared with non-supplemented(NC and PC).The abundance of Cellulosilyticum genera was higher in the BP and ZO treatments rather than in the *** piglets in the NC treatment had the

关键词： Antioxidant Cytokines Diarrhea Fecal score Inflammation Microbiota proteobacteria

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Evidence for a con served microbiota across the different developmental stages of Plodia interpunctella

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Insect Science 2019年第3期26卷 466-478页

作者： Valeria Mereghetti Bessem Chouaia Lidia Limonta Daria Patrizia Locatelli Matteo Montagna Dipartimento di Scienze Agrarie e Ambientali Universita degli Studi di Milano Milan Italy Dipartimento di Scienze per gli Alimenti la Nutrizione I'Ambiente Universita degli Studi di Milano Milan Italy

Diversity and composition of lepidopteran microbiotas are poorly investigated, especially across the different developmental stages. To improve this knowledge, we characterize the microbiota among different developmental stages of the Indian meal moth, Plodia interpunctella, which is considered one of the major pest of commodities world-wide. Using culture-independent approach based on Illumina 16S rRNA gene sequencing we characterized the microbiota of four developmental stages: eggs, first-, and last-instar larvae, and adult. A total of 1022 bacterial OTUs were obtained, showing a quite diversified microbiota associated to all the analyzed stages. The microbiotas associated with P. interpunctella resulted almost constant throughout the developmental stages, with approximately 77% of bacterial OTUs belonging to the phylum of proteobacteria. The dominant bacterial genus is represented by Burkholderia (?64%), followed by Propionibacterium, Delftia, Pseudomonas, and Stenotrophomonas. A core bacterial community, composed of 139 OTUs, was detected in all the developmental stages, among which 112 OTUs were assigned to the genus Burkholderia. A phylogenetic reconstruction, based on the 16S rRNA, revealed that our Burkholderia OTUs clustered with Burkholderia cepacia complex, in the same group of those isolated from the hemipterans Gossyparia spuria and Acanthococcus aceris. The functional profiling, predicted on the base of the bacterial 16S rRNA, indicates differences in the metabolic pathways related to metabolism of amino acids between preimaginal and adult stages. We can hypothesize that bacteria may support the insect host during preimaginal stages.

关键词： Burkholderia Illumina sequencing Indian meal moth insect symbiosis proteobacteria

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Liver tissue microbiota in nonalcoholic liver disease:a change in the paradigm of host-bacterial interactions

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Hepatobiliary Surgery and Nutrition 2021年第3期10卷 337-349页

作者： Silvia Sookoian Carlos J.Pirola School of Medicine Institute of Medical Research A LanariUniversity of Buenos AiresCiudad Autónoma de Buenos AiresArgentina Department of Clinical and Molecular Hepatology Institute of Medical Research(IDIM)National Scientific and Technical Research Council(CONICET)University of Buenos AiresCiudad Autónoma de Buenos AiresArgentina Department of Molecular Genetics and Biology of Complex Diseases Institute of Medical Research(IDIM)National Scientific and Technical Research Council(CONICET)University of Buenos AiresCiudad Autónoma de Buenos AiresArgentina

Nonalcoholic fatty liver disease(NAFLD)pathogenesis is explained by the complex relationship among diet and lifestyle-predisposing factors,the genetic variance of the nuclear and mitochondrial genome,associated phenotypic traits,and the yet not fully explored interactions with epigenetic and other environmental factors,including the *** the wealth of knowledge gained from molecular and genome-wide investigations in patients with NAFLD,the precise mechanisms that explain the variability of the histological phenotypes are not fully *** studies of the gut microbiota in patients with NAFLD and nonalcoholic steatohepatitis(NASH)provided clues on the role of the fecal microbiome in the disease ***,the composition of the gut microbiota does not fully explain tissue-specific mechanisms associated with the degree of disease severity,including liver inflammation,ballooning of hepatocytes,and *** liver acts as a key filtration system of the whole body by receiving blood from the hepatic artery and the portal ***,not only microbes would become entrapped in the complex liver anatomy but,more importantly,bacterial derived products that are likely to be potentially powerful stimuli for initiating the inflammatory ***,the study of liver tissue microbiota offers the opportunity of changing the paradigm of host-NAFLD-microbial interactions from a“gut-centric”to a“liver-centric”***,we highlight the evidence on the role of liver tissue bacterial DNA in the biology of NAFLD and ***,we provide evidence of metagenomic findings that can serve as the seed of further hypothesis-raising studies as well as can be leveraged to discover novel therapeutic targets.

关键词： Nonalcoholic fatty liver disease(NAFLD) nonalcoholic steatohepatitis(NASH) HSD17B13 microbiota microbiome proteobacteria lipopolysaccharide(LPS) drug prediction

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单室微生物电解池除镍途径分析及微生物群落动态特征

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微生物学报 2016年第11期56卷 1794-1801页

作者：赵欣吴忆宁王岭李伟明靳敏李帅哈尔滨工业大学市政环境工程学院黑龙江哈尔滨150090 哈尔滨工业大学城市水资源和水环境国家重点实验室黑龙江哈尔滨150090

【目的】为探究UASB颗粒污泥启动的单室微生物电解池(Single-chamber microbial electrolysis cell,SMEC)对Ni(II)的去除途径和SMEC中微生物群落的动态特征。【方法】以乙酸钠为底物,采用单因子控制方法分析SMEC对Ni(II)的去除途径和应... 详细信息

【目的】为探究UASB颗粒污泥启动的单室微生物电解池(Single-chamber microbial electrolysis cell,SMEC)对Ni(II)的去除途径和SMEC中微生物群落的动态特征。【方法】以乙酸钠为底物,采用单因子控制方法分析SMEC对Ni(II)的去除途径和应用Illumina高通量测序技术解析SMEC启动过程中微生物群落的组成和结构动态学特征。【结果】结果表明,SMEC对重金属的去除主要通过吸附和微生物作用。经培养驯化功能菌群发生变化。成熟单室微生物燃料电池(Single-chamber microbial fuel cell,SMFC)阳极生物膜菌群主要是proteobacteria(变形菌门,91.42%)中的Geobacter sp.(地杆菌属,76.25%);阴极生物膜菌群主要是Bacteroidetes(拟杆菌门,47.99%)中的Niabella sp.(布鲁氏菌属,33.01%)和proteobacteria(45.74%)中的Ochrobactrum sp.(苍白杆菌属,10.80%)。成熟SMFC改装成的SMEC在12.5 mg-Ni(II)/L下,阳极生物膜菌群由单一优势菌Geobacter sp.转变为Geobacter sp.(41.56%)和proteobacteria中的Azospirillum sp.(固氮螺菌属,5.97%);阴极生物膜菌群由Niabella sp.和Ochrobactrum sp.转变为Firmicutes(厚壁菌门,25.21%)中的Acetoanaerobium sp.(19.28%)、proteobacteria(51.42%)中的Dokdonella sp.(16.48%)和Azospirillum sp.(9.49%)。【结论】本研究表明,污泥微生物经SMFC和SMEC驯化过程及Ni(II)的淘汰和选择,在电极上形成了稳定、高效产电与除镍菌群,优势菌群为proteobacteria。

关键词：单室微生物电解池除镍 Illumina高通量测序菌群结构环境的选择性 proteobacteria

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Uranium Bio-Transformations: Chemical or Biological Processes?

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Open Journal of Inorganic Chemistry 2017年第2期7卷 28-60页

作者： Erica L.-W. Majumder Judy D. Wall Department of Biochemistry University of Missouri Columbia MO USA

Uranium bio-transformations are the many and varying types of interactions that microbes can have with uranium encountered in their environment. In this review, bio-transformations, including reduction, oxidation, respiration, sorption, mineralization, accumulation, precipitation, biomarkers, and sensors are defined and discussed. Consensus and divergences are noted in bioavailability, mechanism of uranium reduction, environment, metabolism and the type of organism. The breadth of organisms with characterized bio-trans formations is also cataloged and discussed. We further debate if uranium biotransformations provide bio-protection or bio-benefit to the microbe and highlight the need for more work in the field to understand if microbes use uranium reduction for energy gain and growth, as having the ability is separate from exercising it. The presentation centers on the fundamental drivers for these processes with an additional exposition of the essential contribution of inorganic chemistry techniques to the molecular characterization of these biological processes.

关键词： Uranium Reduction Bio-Sorption proteobacteria

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Temperature Gradient Gel Electrophoresis as a Valuable Accessory Tool for Assessment of Dysbiosis in Crohn’s Disease

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Advances in Microbiology 2016年第8期6卷 549-554页

作者： Vanessa Rafaela de Carvalho Rogeria Keller Ana Carolina da Silva Santos Josias Rodrigues Laboratory of Medical Bacteriology Department of Microbiology and Immunology Institute of Biosciences of the State University of Sao Paulo (UNESP) Botucatu Brazil University of Western Sao Paulo Presidente Prudente Brazil

Escherichia coli and other proteobacteria are augmented and several other bacteria are diminished in Crohn’s (CD) disease patients’ intestine. This imbalance in bacterial species composition—termed dysbiosis—seems to be determinant of CD manifestation. Since a great part of intestinal bacteria are not cultivable, detection of CD dysbiosis is accomplished by molecular tools, involving sequences analysis of the 16SrRNA gene (16SrDNA) present in the patient’s clinical samples, which can be done by sequencing or electrophoresis in denaturing gels of 16SrDNA amplicons. By analyzing, by temperature gradient gel electrophoresis (TGGE) and next generation sequencing of 16SV6-V8rDNA amplicons present in gram negative cultures from four distinct clinical samples of a control subject and a CD patient, this study demonstrates that both techniques were able to detect E. coli overgrowth and reduction in species richness in CD and that TGGE can discriminate sequences collectively labeled as “unclassified” in 16SrDNA databases. Although TGGE per se does not identify the sequences, the discriminatory power that it confers represents valuable accessory information to next generation DNA sequencing (NGS), and as such must be used as a NGS complementary tool.

关键词： Dysbiosis proteobacteria Escherichia coli Crohn’s Disease

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