Category Archives: Human gut

May 10, 2018

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Today we have quite a few interesting papers in “Water microbiome”, there you can read about: drift in the community structuring of bacteria and microbial eukaryotes by R.Logares; phylogeny‐based database “EukRef–Ciliophora” by V. Boscaro;  diverse bacterial and viral populations in agricultural freshwater pond by J. Chopyk. In a “Bioinformatics” section you can read about “MIMOSA: Algorithms for Microbial Profiling” (by O. U. Nalbantoglu) and about use of SplinectomeR package in longitudinal microbiome studies by R.R. Shields- Cutler. Enjoy!

Jobs

PhD position for anaerobic microbiology of the Black Sea, Netherlands

General microbiome

Cargo Transport Shapes the Spatial Organization of a Microbial Community – Abhishek Shrivastava – bioRxiv

The Effect of Berberine on the Transcriptome and Proteome of E. coli – Zhang Shilei – bioRxiv

Predator-by-Environment Interactions Mediate Bacterial Competition in the Dictyostelium discoideum Microbiome – R. Fredrik Inglis – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Diversity time-period and diversity-time-area relationships exemplified by the human microbiome – Zhanshan (Sam) Ma – Scientific Reports

Pregnancy and early life

Microbial Biomarkers of Intestinal Barrier Maturation in Preterm Infants – Bing Ma – bioRxiv

Influence of human milk oligosaccharides on adherence of bifidobacteria and clostridia to cell lines – Musilova Sarka  – Acta Microbiologica et Immunologica Hungarica

 

Oral microbiome

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Glycemic Status Affects the Subgingival Microbiome of Diabetic Patients – Priscila Larcher Longo – Journal of Clinical Periodontology

Research on oral microbiota of monozygotic twins with discordant caries experience – in vitro and in vivo study – Hongle Wu – Scientific Reports

Human gut microbiome

Fecal microbiota transplantation in experimental ulcerative colitis reveals associated gut microbial and host metabolic reprogramming – Zhixiang Yan – Applied and Environmental Microbiology

Fecal microbiota transplantation treatment for refractory ulcerative colitis with allergy to 5-aminosalicylic acid: A case report – Hong-Gang Wang – Medicine

Review: Influence of Commensal Microbiota on the Enteric Nervous System and Its Role in Neurodegenerative Diseases – Endres K. – Journal of Innate Immunology

Loss of Ethanolamine Utilization in Enterococcus faecalis Increases Gastrointestinal Tract Colonization – Karan Gautam Kavala – mBio

Compositional and Functional Differences in the Human Gut Microbiome Correlate with Clinical Outcome following Infection with Wild-Type Salmonella enterica Serovar Typhi – Yan Zhang – mBio

Animal experiments

Effects of gut microbiota and time of treatment on tissue levels of green tea polyphenols in mice – Anna B. Liu – BioFactors

Gastrointestinal microbiota and mucosal immune gene expression in neonatal pigs reared in a cross-fostering model – Nidia Maradiaga – Microbial Pathogenesis

Prolonged restraint stressor exposure in outbred CD-1 mice impacts microbiota, colonic inflammation, and short chain fatty acids – Ross M. Maltz – PLOS One

Review: Biomarkers for monitoring intestinal health in poultry: present status and future perspective – Richard Ducatelle – Veterinary Research

Animal microbiome 

Near full-length 16S rRNA gene next-generation sequencing revealed Asaia as a common midgut bacterium of wild and domesticated Queensland fruit fly larvae – Ania T. Deutscher – Microbiome

Crown-of-thorns sea star, Acanthaster cf. solaris, have tissue-characteristic microbiomes with potential roles in health and reproduction – Lone Høja – Applied and Environmental Microbiology

Multilevel social structure and diet shape the gut microbiota of the gelada monkey, the only grazing primate – Pål Trosvik – Microbiome

Antimicrobial activity in culturable gut microbial communities of springtails – Valeria Agamennone  – Journal of Applied Microbiology

Diversity and antimicrobial potential in sea anemone and holothurian microbiomes – Elizabeth León-Palmero  – PLOS One

Plant, root, and soil microbiome

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Core microbiomes for sustainable agroecosystems – Toju H -Nature Plants

Determination of agricultural impact on soil microbial activity using δ18OP HCl and respiration experiments – Katherine Polain – ACS Earth and Space Chemistry

Seasonal dynamics of bacterial communities in a Betula albosinensis forest – C. Du – European Journal of Soil Science

Niche partition of phenanthrene-degrading bacteria along a Phragmites australis rhizosphere gradient – Xiaofei Lv – Biology and Fertility of Soils

Water and extremophile microbiome

Effects of Xiantao sewage treatment on microbial community structure of shallow groundwater in wetland – Shu-Fen Song – bioRxiv

Unexpected versatility in the metabolism and ecophysiology of globally relevant nitrite-oxidizing Nitrotoga bacteria – Andrew Boddicker – bioRxiv

Long-term seasonality of marine photoheterotrophic bacteria reveals low cohesiveness within the different phylogroups – Adrià Auladell – bioRxiv

Molecular cloning of glutathione peroxidase gene of Antarctic ice microalga Chlamydomonas sp. ICE‐L and its expression changes under temperature and salinity stress – Jin Hui Wang – Phycological Research

Contrasting prevalence of selection and drift in the community structuring of bacteria and microbial eukaryotes – Ramiro Logares – Environmental Microbiology

EukRef–Ciliophora: A manually curated, phylogeny‐based database of small subunit rRNA gene sequences of ciliates – Vittorio Boscaro – Environmental Microbiology

Novel human-associated Lachnospiraceae genetic markers improve detection of fecal pollution sources in urban waters – Shuchen Feng – Applied and Environmental Microbiology

Municipal wastewater treatment potential and metal accumulation strategies of Colocasia esculenta (L.) Schott and Typha latifolia L. in a constructed wetland – Vivek Rana – Environmental Monitoring and Assessment

Agricultural Freshwater Pond Supports Diverse and Dynamic Bacterial and Viral Populations – Jessica Chopyk – Frontiers in Microbiology / Aquatic Microbiology

Characterization of a Highly Enriched Microbial Consortium Reductively Dechlorinating 2,3-Dichlorophenol and 2,4,6-Trichlorophenol and the Corresponding cprA Genes from River Sediment – Wael S. El-Sayed – Polish Journal of Microbiology

Built environment

Characterization of fungi in office dust: comparing results of microbial secondary metabolites, fungal ITS region sequencing, viable culture, and other microbial indices – Ju Hyeong Park – Indoor Air

Investigation of the Active Biofilm Communities on Polypropylene Filter Media in a Fixed Biofilm Reactor for Wastewater Treatment – Iffat Naz – Journal of Chemical Technology and Biotechnology

Food microbiology

Characterization of the contaminant bacterial communities in sugarcane first-generation industrial ethanol production – Maria L. Bonatelli – FEMS Microbiology Letters

Probiotics / prebiotics

Phylotype-level profiling of lactobacilli in highly complex environments by means of an ITS-based metagenomic approach – Christian Milani – Applied and Environmental Microbiology

Comparative Genomics Reveals the Regulatory Complexity of Bifidobacterial Arabinose and Arabino-Oligosaccharide Utilization – Aleksandr A. Arzamasov – Frontiers in Microbiology /Evolutionary and Genomic Microbiology

 

Bioinformatics

MIMOSA: Algorithms for Microbial Profiling – Ozkan Ufuk Nalbantoglu – IEEE/ACM Transactions on Computational Biology and Bioinformatics

SplinectomeR Enables Group Comparisons in Longitudinal Microbiome Studies – Robin R. Shields-Cutler – Frontiers in Microbiology / Systems Microbiology

Metagenome enrichment approach used for selection of oil-degrading bacteria consortia for drill cutting residue bioremediation – Alaine B.Guerra – Environmental Pollution

Biotechnology

Microbial co-culturing systems: butanol production from organic wastes through consolidated bioprocessing – Yujia Jiang – Applied Microbiology and Biotechnology

Techniques

Sensitive detection of Live Escherichia coli by bacteriophage amplification-coupled immunoassay on the Luminex® MAGPIX instrument – Tomotaka Mido – bioRxiv

Microbes in the news

Scientists use dietary seaweed to manipulate gut bacteria in mice

Microbes are savvy investors when contributing to the common good

 

May 9, 2018

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Have a good Wednesday! Today, we have an interesting set of papers about the effect of different compounds on microbiota, as well the effect of some probiotics. We have also a paper about the use binding of  immunoglobulin A by gut microbiota commensals as a potential mechanism for stabilization; we have also papers about virome from urinary and female reproductive tracts, a study a multi-site study of maternal microbiota.

Gut and General Microbiome

Introduction: The host-associated microbiome: Pattern, process and function – Laura Wegener Parfrey – Molecular Ecology (Special Issue: The host-associated microbiome: Pattern, process and function)

Gut microbiota utilize immunoglobulin A for mucosal colonization – G. P. Donaldson – Science

Low Maternal Microbiota Sharing across Gut, Breast Milk and Vagina, as Revealed by 16S rRNA Gene and Reduced Metagenomic Sequencing – Ekaterina Avershina – Genes

Editorial: Bacteria in the ageing gut: Did the taming of fire promote a long human lifespan? – Antoine Danchin – Environmental Microbiology

Commentary: Insights into the role of gut microbiota in obesity: pathogenesis, mechanisms, and therapeutic perspectives – Lijuan Sun – Protein & Cell

Review: Gut microbiota derived metabolites in cardiovascular health and disease – Zeneng Wang – Protein & Cell

Treating Clostridium difficile infections: Should fecal microbiota transplantation be reclassified from investigational drug to human tissue? – Mark Stuntz – Contemporary Clinical Trials Communications

Effects of intestinal colonization by Clostridium difficile and Staphylococcus aureus on microbiota diversity in healthy individuals in China – Danfeng Dong – BMC Infectious Diseases

BaiCD gene cluster abundance is negatively correlated with Clostridium difficile infection – Philipp Solbach – PLoS ONE

Microbiome Responses to an Uncontrolled Short-Term Diet Intervention in the Frame of the Citizen Science Project – Natalia S. Klimenko – Nutrients

Respiratory Tract Microbiome

Relation between lower respiratory tract microbiota and type of immune response against tuberculosis – Maede Nakhaee – Microbial Pathogenesis

Microbiome characteristics of induced sputum compared to bronchial fluid and upper airway samples – Shi‐qi An – Pediatric Pulmonology

The association between inflammation, the microbiome and urethane-induced pulmonary adenocarcinoma – Zenghua Deng – Oncology Letters

Urinary/Reproductive Tract Microbiome

Urinary Virome Perturbations in Kidney Transplantation – Tara K. Sigdel – Frontiers in Medicine

The Vaginal Eukaryotic DNA Virome and Preterm Birth – Kristine M. Wylie – American Journal of Obstetrics and Gynecology

Beneficial Microbes and Compounds

Walnut Consumption Alters the Gastrointestinal Microbiota, Microbially Derived Secondary Bile Acids, and Health Markers in Healthy Adults: A Randomized Controlled Trial – Hannah D Holscher – The Journal of Nutrition

The effect of vitamin D on intestinal inflammation and faecal microbiota in patients with ulcerative colitis – Mayur Garg – Journal of Crohn’s and Colitis

Exopolysaccharide from Bifidobacterium longum subsp. longum 35624™ modulates murine allergic airway responses – E. Schiavi – Beneficial Microbes

Modulatory effect of three probiotic strains on infants’ gut microbial composition and immunological parameters on a placebo-controlled, double-blind, randomised study – J. De Andrés – Beneficial Microbes

Review: Role of Lactobacillus reuteri in Human Health and Diseases – Qinghui Mu – Frontiers in Microbiology

Intake of phytic acid and myo-inositol lowers hepatic lipogenic gene expression and modulates gut microbiota in rats fed a high-sucrose diet – Yukako Okazaki – Biomedical Reports

Animal Microbiome

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – Scientific Reports

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Endophytic Fungi in Species of Artemisia – Andreea Cosoveanu – Journal of Fungi

Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice – Hao Guo – Environmental Toxicology and Pharmacology

Food Microbiome

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms – Van Thi Thuy Ho – International Journal of Food Microbiology

Validation of standard method EN ISO 22964:2017 – Microbiology of the food chain – Horizontal method for the detection of Cronobacter spp – Amparo de Benito – International Journal of Food Microbiology

Plant and Soil Microbiome

Mycobiome analysis of asymptomatic and symptomatic Norway spruce trees naturally infected by the conifer pathogens Heterobasidion spp. – Andriy Kovalchuk – Environmental Microbiology Reports

Perspective: Core microbiomes for sustainable agroecosystems – Hirokazu Toju – Nature Plants

Meetings: Holobiont: a conceptual framework to explore the eco-evolutionary and functional implications of host-microbiota interactions in all ecosystems – Denis Faure – New Phytologist

Other

Marker microbiome clusters are determined by operational parameters and specific key taxa combinations in anaerobic digestion – Susanne Theuerl – Bioresource Technology

 

May 6, 2018

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Brassicaceae plants-fungi associations, a feature on PCR bias during microbiome analysis, a thesis about viruses; preprints about Mobile-CRISPRi system on bacteria, what may happen to the intestinal microbiota when Lactobacillus reuteri intervenes; few non-microbio picks covering mental health, conservation policy, stem cell policy; and a lot more for our digest from Sunday.

General microbiome

Preprint: Mobile-CRISPRi: Enabling Genetic Analysis of Diverse Bacteria – JM Peters – bioRxiv

Preprint: Effect of Lactobacillus reuteri on intestinal microflora and immune parameters: involvement of sex differences – J He – biorXiv

Review: The Interplay Between the Microbiome and Cardiovascular Risk – BA Minnifield – Current Genetic Medicine Reports

Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria – KL Wyres – Current Opinion in Microbiology

Proteomic studies on lactic acid bacteria: A review – KS Vinusha – Biochemistry and Biophysics Reports

Multi-site human microbiome

Distinct shifts in the oral microbiota are associated with the progression and aggravation of mucositis during radiotherapy – J Hou – Radiotherapy and Oncology

Human skin microbiome

Skin microbiome changes in patients with interdigital tinea pedis – R  Wang – British Journal of Dermatology

Human vaginal microbiome

The Vaginal Eukaryotic DNA Virome and Preterm Birth  – KM Wylie – American Journal of Obstetrics and Gynecology

Systematic Review: The vaginal microbiota and its association with Human Papillomavirus, Chlamydia trachomatis, Neisseria gonorrhea and Mycoplasma genitalium infections: a systematic review and meta-analysis – J Tamarelle – Clinical Microbiology and Infection

Human gut microbiome

Review: Methods for studying gut microbiota: A primer for physicians – AN Sarangi – Journal of Clinical and Experimental Hepatology

Review: Effects of the Gut microbiota on Amygdalin and its use as an anti-cancer therapy: Substantial review on the key components involved in altering dose efficacy and toxicity – V Jaiswal – Biochemistry and Biophysics Reports

The ability of human intestinal anaerobes to metabolize different oligosaccharides: Novel means for microbiota modulation? – R Ose – Anaerobe

Clostridium difficile cure with fecal microbiota transplantation in a child with Pompe disease: a case report – DE Dow – Journal of Medical Case Reports

Association Between Bacteremia from Specific Microbes and Subsequent Diagnosis of Colorectal Cancer  – TNY Kwong – Gastroenterology

Animal experiments 

Tributyltin exposure induces gut microbiome dysbiosis with increased body weight gain and dyslipidemia in mice – H Guo – Environmental Toxicology and Pharmacology

Inhibition Effect of Glycyrrhiza Polysaccharide (GCP) on Tumor Growth through Regulation of the Gut Microbiota Composition – X Zhang – Journal of Pharmacological Sciences

Ketogenic diet enhances neurovascular function with altered gut microbiome in young healthy mice – D Ma – Scientific Reports

Preprint: Efficacy of fecal sampling as a gut proxy in the study of chicken gut microbiota – W Yan – bioRxiv

Acute exposure to PBDEs at an environmentally realistic concentration causes abrupt changes in the gut microbiota and host health of zebrafish – L Chen – Environmental Pollution

Animal microbiome 

Integrated metatranscriptomics and metaproteomics for the characterization of bacterial microbiota in unfed Ixodes ricinus – A Hernández-Jarguín – Ticks and Tick-borne Diseases

Metatranscriptome analysis of the intestinal microorganisms in Pardosa pseudoannulata in response to cadmium stress – H Yang – Ecotoxicology and Environmental Safety

Plant, root, and soil microbiome

Beneficial associations between Brassicaceae plants and fungal endophytes under nutrient-limiting conditions: evolutionary origins and host–symbiont molecular mechanisms – K Hiruma – Current Opinion in Plant Biology

Cross-kingdom lipid transfer in arbuscular mycorrhiza symbiosis and beyond – A Keymer – Current Opinion in Plant Biology

Isolation of local Bacillus spp. from Afghanistan soils and their potential in suppressing the root-knot nematodes on tomato – AS Jamily – J-Stage

Effect of community-based soil and water conservation practices on arbuscular mycorrhizal fungi types, spore densities, root colonization, and soil nutrients in the northern highlands of Ethiopia – M Welemariam – Chemical and Biological Technologies in Agriculture

Biocontrol mechanisms of Bacillus sp., isolated from tomato rhizosphere, against Fusarium oxysporum f. sp. lycopersici – M Jangir – Biological Control

Root Exudates Dominate the Colonization of Pathogen and Plant Growth-Promoting Rhizobacteria – J Yuan – Root Biology

Unfolding the Role of Rhizomicrobiome Toward Sustainable Agriculture – S Kaul – Root Biology

Litter breakdown as a tool for assessment of the efficiency of afforestation and ash-aided phytostabilization on metal-contaminated soils functioning in Northern France – J Leclercq-Dransart – Environmental Science and Pollution Research 

Sugars en route to the roots. Transport, metabolism and storage within plant roots and towards microorganisms of the rhizosphere – N Hennion – Physiologia Plantarum

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient – A Angermeyer – PeerJ

Impact of slope exposure on chemical and microbiological properties of Norway spruce deadwood and underlying soil during early stages of decomposition in the Italian Alps – T Bardelli – CATENA

Built environment 

A comparative study of eubacterial communities by PCR-DGGE fingerprints in anoxic and aerobic biotrickling filters used for biogas desulfurization – A Valle – Bioprocess and Biosystems Engineering

Food microbiology

Microbial community dynamics of Dan’er barley grain during the industrial malting process – X Li – Food Microbiology

Physicochemical, microbiological and sensory acceptance alterations of strawberries caused by gamma radiation and storage time – M de Jesus Filho – Scientia Horticulturae

Evaluation of critical points of mould growth and mycotoxin production in the stored barley ecosystem with a hazardous initial microbiological state of grain – J Wawrzyniak – Journal of Stored Products Research

Viruses and phages

Thesis: Virology By The Numbers: A Quantitative Exploration of Viral Energetics, Genomics, and Ecology – G Mahmoudabadi – Caltech THESIS

 

Techniques

Microbiology: making the best of PCR bias – M  Eisenstein – Nature

Anton Chekhov and Robert Koch Cheek to Cheek: A Proteomic Study – A D’Amato – Proteomics

Microbes in the news

Future of Microbiome Drugs Market including key players Pfizer, Second Genome, Seres Therapeutics – Technical Progress News

Pattern hair loss could be due to gut bacteria – Science Nordic

Legionella bacteria has been detected at the problem-plagued Perth Children’s Hospital. – SBS News

Connections Between Art And Science Explored – The Enterprise

Non-microbiology picks

Arctic ice carries heavy freight of plastic – Nature

Brazil’s lawmakers renew push to weaken environmental rules – Nature

Feeling overwhelmed by academia? You are not alone – Nature

Real-world illness requires medical multitasking – Nature

Announcement: stem-cell policy – Nature

May 4, 2018

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Today we have many interesting news and many papers in “Plant, root, and soil microbiome” section. Enjoy your friday read!

General microbiome

Uncovering the drivers of host-associated microbiota with joint species distribution modeling – Johannes R. Björk – bioRxiv

Competence Inhibition by the XrpA Peptide Encoded Within the comX Gene of Streptococcus mutans – Justin Kaspar – bioRxiv

Microbiota and metabolic diseases – Alessia Pascale – Endocrine

Human respiratory microbiome

The Gut-Lung Axis and Pulmonary Responses to Ozone – Judith A Voynow – American Journal of Respiratory and Molecular Biology

 

Human skin microbiome

Microbial host interactions and impaired wound healing in mice and humans: defining a role for BD14 and NOD2 – Helen Williams – Journal of Investigative Dermatology

Human nearly-sterile sites

The Role of Microbiota in Retinal Disease – Sheldon Rowan – Retinal Degenerative Diseases

Human gut microbiome

Immune Cells and Microbiota Response to Iron Starvation – Marcello Chieppa – Frontiers in Medicine / Gastroenterology

The Role of the Gut Microbiome in Colorectal Cancer – Grace Y. Chen – Clinics in Colon and Rectal Surgery

Enterococcus faecalis AHG0090 is a Genetically Tractable Bacterium and Produces a Secreted Peptidic Bioactive that Suppresses Nuclear Factor Kappa B Activation in Human Gut Epithelial Cells – Páraic Ó Cuív – Frontiers in Immunology /  Microbial Immunology

Animal experiments

Core gut microbiota in Jinhua pigs and its correlation with strain, farm and weaning age – Hua Yang – Journal of Microbiology

Animal microbiome 

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Stochastic processes govern bacterial communities from the blood of pikas and from their arthropod vectors – Huan Li – FEMS Microbiology Ecology

An in vitro evaluation of browser and grazer fermentation efficiency and microbiota using European moose spring and summer foods – Sophie J. Krizsan – Ecology & Evolution

The effect of gut microbiota elimination in Drosophila melanogaster: A how-to guide for host–microbiota studies – Chloe Heys  – Ecology & Evolution

Urea hydrolysis by gut bacteria in a hibernating frog: evidence for urea-nitrogen recycling in Amphibia – James M. Wiebler – Proceedings of the Royal Society B

Plant, root, and soil microbiome

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

Soil metabarcoding identifies season indicators and differentiators of pig and Agrostis/Festuca spp. decomposition – Ayodeji O.Olakanye – Forensic Science International

Modulation of plant chemistry by beneficial root microbiota – Desalegn W. Etalo  –  Natural Product Reports

Highly diverse endophytes in roots of Cycas bifida (Cycadaceae), an ancient but endangered gymnosperm – Ying Zheng – Journal of Microbiology

A global atlas of the dominant bacteria found in soil – Manuel Delgado-Baquerizo – Science

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na –  Frontiers in Microbiology

Combined effects of phosphate-solubilizing bacterium XMT-5 (Rhizobium sp.) and submerged macrophyte Ceratophyllum demersum on phosphorus release in eutrophic lake sediments – Haifeng Li – Environmental Science and Pollution Research

Successful phytoremediation of crude-oil contaminated soil at an oil exploration and production company by plants-bacterial synergism – Kaneez Fatima – International Journal of Phytoremediation

Alginate-perlite encapsulated Pseudomonas putida A (ATCC 12633) cells: preparation, characterization and potential use as plant inoculants – Andrés S. Liffourrena – Journal of Biotechnology

Variations of Bacterial Community Diversity Within the Rhizosphere of Three Phylogenetically Related Perennial Shrub Plant Species Across Environmental Gradients – Xiaofan Na – Frontiers in Microbiology / Terrestrial Microbiology

Water and extremophile microbiome 

Conductive Particles Enable Syntrophic Acetate Oxidation between Geobacter and Methanosarcina from Coastal Sediments – Amelia-Elena Rotaru – mBio

Mind the gut: genomic insights to population divergence and gut microbial composition of two marine keystone species – Katharina Fietz – BMC Microbiome

Enhanced degradation of phenol in floating treatment wetlands by plant-bacterial synergism – Hamna Saleem – International Journal of Phytoremediation

Bacterial community diversity in a full scale biofilter treating wastewater odor – M. J. Allievi – Water Science & Technology

Food microbiology

Sausage fermentation and starter cultures in the era of molecular biology methods – Irene Franciosa – International Journal of Food Microbiology

Contribution of the novel sulfur-producing adjunct Lactobacillus nodensis to flavor development in Gouda cheese – Elaine O’Brien – Journal of Dairy Science

Probiotics / prebiotics

Probiotics drive gut microbiome triggering emotional brain signatures – Deepika Bagga – Gut Microbiome

Phages and viruses

Reactivation of latent HIV-1 in vitro using an alcoholic extract from Euphorbia umbellata (Euphorbiaceae) latex – Ana L Valadao – bioRxiv

Mycobacteria recycle their peptidoglycan via a novel pathway which influences antimicrobial resistance and limits proliferation in macrophages – Patrick J. Moynihan – bioRxiv

Biotechnology

Microbiological aspects of thermophile pretreatment of activated sludge inhibiting electricity generation of microbial fuel cell – Yang-Guo Zhao – Water Science & Technology

Methane-yielding microbial communities processing lactate-rich substrates: a piece of the anaerobic digestion puzzle – Anna Detman – BMC Biotechnology for Biofuels

Microbes in the news 

Researchers find a gene that lets bacteria kill all male flies

Targeting Gut Bacteria to Reduce Disease

Applying live bacteria to skin improves eczema

Walnuts impact gut microbiome and improve health

By wrapping itself in antibodies, this bacterium may become a stable, beneficial part of the gut

A healthy digestive system is all you need in life

 

 

May 3, 2018

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Have a good Thursday! Today, in Microbiome Digest: studies about Bacterial Vaginosis, dysbiosis associated with Hepatitis C infection, oral microbiome and oral cancer, microbiome reestablishment after cleaning, detection of microbes in culture-negative intra-amniotic infections and more…

Human Microbiome and General

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults – Owen Cronin – mSystems

Review: Relationship between diet, the gut microbiota, and brain function – Anouk C Tengeler – Nutrition Reviews

Identification of Key Bacteria Involved in the Induction of Incident Bacterial Vaginosis: A Prospective Study – Christina A Muzny – The Journal of Infectious Diseases

Gut Dysbiosis Associated With Hepatitis C Virus Infection – Takako Inoue – Clinical Infectious Diseases

Research Highlight: Fibre aids fight against nasty gut infection – Nature

Review: The Intestinal Epithelium: Central Coordinator of Mucosal Immunity – Joannie M. Allaire – Trends in Immunology

Humans as holobionts: implications for prevention and therapy -Maarten van de Guchte – Microbiome

Obese Subjects With Specific Gustatory Papillae Microbiota and Salivary Cues Display an Impairment to Sense Lipids – Philippe Besnard – Scientific Reports

Bacterial culture-negative subclinical intra-amniotic infection can be detected by bacterial 16S ribosomal DNA-amplifying polymerase chain reaction – Sachi Morimoto – Japanese Journal of Infectious Diseases

Impact of HIV and Type 2 diabetes on Gut Microbiota Diversity, Tryptophan Catabolism and Endothelial Dysfunction – Hedda Hoel – Scientific Reports

New Horizons in Obstructive Lung Disease. Microbiome Dynamics, Pulmonary Artery Enlargement, and Endobronchial Valves – Pujan H. Patel – American Journal of Respiratory and Critical Care Medicine

Oral Microbiota Community Dynamics Associated With Oral Squamous Cell Carcinoma Staging – Chia-Yu Yang – Frontiers in Microbiology

Bifidobacterium longum subsp infantis CECT7210-supplemented formula reduces diarrhea in healthy infants: a randomized controlled trial – Joaquin Escribano – Pediatric Research

 

Animal Microbiome

Transplantation of human microbiota into conventional mice durably reshapes the gut microbiota – Laura Wrzosek – Scientific Reports

Restructuring of the Gut Microbiome by Intermittent Fasting Prevents Retinopathy and Prolongs Survival in db/db Mice – Eleni Beli – Diabetes

Effects of shenling baizhu powder herbal formula on intestinal microbiota in high-fat diet-induced NAFLD rats – Yupei Zhang – Biomedicine & Pharmacotherapy

The effects of sewage treatment plant effluents on hepatic and intestinal biomarkers in common carp (Cyprinus carpio) – Sidika Sakalli – Science of The Total Environment

Feminizing Wolbachia influence microbiota composition in the terrestrial isopod Armadillidium vulgare – Jessica Dittmer – Scientific Reports

Preprint: Intestinal microbiota of whitefish (Coregonus sp.) species pairs and their hybrids in natural and controlled environment – Maelle Sevellec – bioRxiv

Gut microbiomes of wild great apes fluctuate seasonally in response to diet – Allison L. Hicks – Nature Communications

Dietary polyphenols enhance optogenetic recall of fear memory in hippocampal dentate gyrus granule neuron subpopulations – Chad Smith – Communications Biology

 

Built Environments

The Reestablishment of Microbial Communities after Surface Cleaning in Schools – Sarah E. Kwan – Journal of Applied Microbiology

 

Bioinformatics and Genomics

SHI7 Is a Self-Learning Pipeline for Multipurpose Short-Read DNA Quality Control – Gabriel A. Al-Ghalith – mSystems

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information – Stefan Janssen – mSystems

Identifying Group-Specific Sequences for Microbial Communities Using Long k-mer Sequence Signatures – Ying Wang – Frontiers in Microbiology

 

Plant/Soil Microbiomes

The role of bacteria in pine wilt disease: insights from microbiome analysis – Marta Alves – FEMS Microbiology Ecology

 

Other (Microbiome-related)

Review: Food Intake and Eating Behavior After Bariatric Surgery – Werd Al-Najim – Physiological Reviews

Review: Microfluidic Organ-on-a-Chip Models of Human Intestine – Amir Bein – Cellular and Molecular Gastroenterology and Hepatology

Preprint: CRISPR-Cas blocks antibiotic resistance plasmid transfer between Enterococcus faecalis strains in the gastrointestinal tract – Valerie J Price – bioRxiv

 

May 2, 2018

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In our 2nd May Digest there are many interesting Jobs, News and papers, among which few recommendations: the review on human oral microbiota by Yangheng Zhang, bacterial versus human thymidylate synthas by Zahidul Islam, gut metabolome meets microbiome by Santosh Lamichhane and GET_PHYLOMARKERS – a new software package for phylogenomics and inferring pan-genome phylogenies. Enjoy!

Jobs

Research assistant in Microbial Systems and Synthetic Biology, University of Amsterdam, the Netherlands

Research Scientist Engineer, University of Washington, WA, US

Post-Doctoral Research Scientist – Molecular Biology/Biochemistry, Rothamsted Research, Harpenden, UK

Post-doc position, Universite Bourgogne Franche-Comté, Dijon, France

General microbiome

Novel Antimicrobials for the Treatment of Clostridium difficile Infection – Nicola Petrosillo – Frontiers in Medicine

Metagenomic assessment of the interplay between the environment and the genetic diversification of Acinetobacter – Marc Garcia-Garcera – Environmental Microbiology

Further expansion of methane metabolism in the Archaea – Yulin Wang – bioRxiv

Bacterial versus human thymidylate synthase: Kinetics and functionality – Zahidul Islam – PLOS One

Humans as holobionts: implications for prevention and therapy – Maarten van de Guchte – Microbiome

Genomewide characterisation of the genetic diversity of carotenogenesis in bacteria of the order Sphingomonadales – Shivakumara Siddaramappa – Microbial Genomics

Pregnancy and early life

Spleen development is modulated by neonatal gut microbiota – M. Manuela Rosado – Immunology Letters

HIV antiretroviral exposure in pregnancy induces detrimental placenta vascular changes that are rescued by progesterone supplementation – Hakimeh Mohammadi – Scientific Reports

Human respiratory microbiome

Biological exacerbation clusters demonstrate asthma and COPD overlap with distinct mediator and microbiome profiles  – Michael A. Ghebre – Journal of Allergy and Clinical Immunology

Oral microbiome

Review: Human oral microbiota and its modulation for oral health – Yangheng Zhang – Biomedicine & Pharmacotherapy

Oral Administration of Probiotics Increases Paneth Cells and Intestinal Antimicrobial Activity – Silvia I. Cazorla – Frontiers in Microbiology /Food Microbiology

Oral microbiota reveals signs of acculturation in Mexican American women – Kristi L. Hoffman – PLOS One

Human gut microbiome

Gut metabolome meets microbiome: A methodological perspective to understand the relationship between host and microbe – Santosh Lamichhane – Methods

Linking gut microbiota to cardiovascular disease and hypertension: Lessons from chronic kidney disease – B. Meijers – Pharmacological Research

PGRP-LB homolog acts as a negative modulator of immunity in maintaining the gut-microbe symbiosis of red palm weevil, Rhynchophorus ferrugineus Olivier – Bishnu Dawadi – Developmental & Comparative Immunology

Imbalance of gut microbiome and intestinal epithelial barrier dysfunction in cardiovascular disease  – Judith N. Lezutekong – Clinical Science

Intestinal Immunomodulatory Cells (T Lymphocytes): A Bridge between Gut Microbiota and Diabetes – Qingwei Li – Mediators of Inflammation

In Vitro Fermentation Behaviour of Isomalto/Malto‐Polysaccharides Using Human Faecal Inoculum Indicates Prebiotic Potential – Fangjie Gu – Molecular Nutrition & food Research

A repeat offender: Recurrent extraintestinal Clostridium difficile infection following fecal microbiota transplantation – Bradley J.Gardiner – Anaerobe

Illuminating the microbiome’s dark matter: a functional genomic toolkit for the study of human gut Actinobacteria – Jordan E Bisanz – bioRxiv

Animal experiments

Astragalus affects fecal microbial composition of young hens as determined by 16S rRNA sequencing – Hongxing Qiao – AMB Express

Omeprazole Minimally Alters the Fecal Microbial Community in Six Cats: A Pilot Study – Sarah M. Schmid – Frontiers in Veterinary Science

Resveratrol Prevents the Development of Hypertension Programmed by Maternal Plus Post‐Weaning High‐Fructose Consumption Through Modulation of Oxidative Stress, Nutrient‐Sensing Signals, and Gut Microbiota – You-Lin Tain – Molecular Nutrition & Food Research

DNA microarray-based assessment of virulence potential of Shiga toxin gene-carrying Escherichia coli O104:H7 isolated from feedlot cattle feces – Pragathi B. Shridhar – PLOS One

Animal microbiome

Comparative metabolomics of aging in a long-lived bat: Insights into the physiology of extreme longevity – Hope C. Ball – PLOS One

Plant, root, and soil microbiome

Identification of chemotaxis compounds in root exudates and their sensing chemoreceptors in plant growth-promoting rhizobacteria Bacillus amyloliquefaciens SQR9 – Haichao Feng – Molecular Plant-Microbe Interactions

Shared strategies for β-lactam catabolism in the soil microbiome – Terence S. Crofts – Nature Chemical Biology

Review: Molecular networks in plant-pathogen holobiont – Tatsuya Nobori – FEBS Letters

Importance of Soil Temperature for the Growth of Temperate Crops under a Tropical Climate and Functional Role of Soil Microbial Diversity – Nurul Syazwani Ahmad Sabri – Microbes and Environments

The Impact of Remediation Through Stabilizing Amendments on Taxonomic and Metabolic Patterns of Bacteria and Archaea in Cadmium-Contaminated Paddy Fields in Southwestern China – Yi Chen – bioRxiv

Cas9/CRISPR genome editing to demonstrate the contribution of Cyp51A Gly138Ser to azole resistance in Aspergillus fumigatus – Takashi Umeyama – bioRxiv

Short-term microbial effects of a large-scale mine-tailing storage facility collapse on the local natural environment – Heath W. Garris –  PLOS One

Water and extremophile microbiome 

Effect of the natural arsenic gradient on the diversity and arsenic resistance of bacterial communities of the sediments of Camarones River (Atacama Desert, Chile) – Carla G. Leon – PLOS One

The association of diet, gut microbiota and colorectal cancer: what we eat may imply what we get – Jia Yang – Protein & Cell

Marine-influenced microbial communities inhabit terrestrial hot springs on a remote island volcano – Lucy C. Stewart – Extremophiles

Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community – Vitaly V. Kadnikov – Scientific Reports

Effects of Fecal Source Input, Environmental Conditions, and Environmental Sources on Enterococci Concentrations in a Coastal Ecosystem – Derek Rothenheber – bioRxiv

Precipitation of Calcium Carbonate Mineral Induced by Viral Lysis of Cyanobacteria – Hengchao Xu – Biogeosciences

Food microbiology

Probiotic and Technological Properties of Exopolysaccharide Producing Lactic Acid Bacteria Isolated from Cereal-based Nigerian Fermented Food Products – A.T. Adesulu-Dahunsi – Food Control

Phages and viruses

Human enteric bacteria and viruses in five wastewater treatment plants in the Eastern Cape, South Africa – Olayinka Osuolale – Journal of Infection and Public Health

Dissecting the herpesvirus architecture by targeted proteolysis – Gina Rose Daniel – bioRxiv

Bioinformatics

GET_PHYLOMARKERS, a Software Package to Select Optimal Orthologous Clusters for Phylogenomics and Inferring Pan-Genome Phylogenies, Used for a Critical Geno-Taxonomic Revision of the Genus Stenotrophomonas – Pablo Vinuesa – Frontiers in Microbiology / Evolutionary and Genomic Microbiology

Bioenergy

Genome-centric metatranscriptomes and ecological roles of the active microbial populations during cellulosic biomass anaerobic digestion – Yangyang Jia – Biotechnology for Biofuels

Meta-proteomic analysis of protein expression distinctive to electricity-generating biofilm communities in air-cathode microbial fuel cells – Jeremy F. Chignell – Biotechnology for Biofuels

Metagenome, metatranscriptome, and metaproteome approaches unraveled compositions and functional relationships of microbial communities residing in biogas plants – Julia Hassa – Applied Microbiology and Biotechnology

Mini Review: New concepts in anaerobic digestion processes: recent advances and biological aspects – Antonio Castellano-Hinojosa – Applied Microbiology and Biotechnology

Genome comparison of different Zymomonas mobilis strains provides insights on conservation of the evolution – Chen Chen – PLOS One

Microbes in the news

Microbes living in a toxic volcanic lake could hold clues to life on Mars

Researchers Finally Figure Out How Vaping Impacts Your Gut Bacteria

Bacteria eat antibiotics, and warn each other of threats

 

April 29, 2018

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Today’s digest has some interesting stuffs on vaginal microbiota, MRSA, AMF, microbes inside a library and lots more to get you through the weekend!

General microbiome

Marine sponge microbial association: Towards disclosing unique symbiotic interactions – GS Kiran – Marine Environmental Research

Multi-site human microbiome

The majority of MRSA colonized children not given eradication treatment are still colonized one year later. Systemic antibiotics improve the eradication rate – J Jörgensen – Infectious Diseases

Human respiratory microbiome

Biological exacerbation clusters demonstrate asthma and COPD overlap with distinct mediator and microbiome profiles  – MA Ghebre – Journal of Allergy and Clinical Immunology

Human vaginal microbiome

Assessment of microbiota:host interactions at the vaginal mucosa interface – P Pruski – Methods

Human gut microbiome

Review: New concepts on intestinal microbiota and the role of the non-absorbable antibiotics with special reference to rifaximin in digestive diseases – JS Bajaj – Digestive and Liver Disease

Review: Determinants of IBD Heritability: Genes, Bugs, and More – W Turpin – Inflammatory Bowel Diseases

Fecal microbiome from patients with ulcerative colitis is potent to induce inflammatory responses – S Wang – International Immunopharmacology

A Prospective Metagenomic and Metabolomic Analysis of the Impact of Exercise and/or Whey Protein Supplementation on the Gut Microbiome of Sedentary Adults – O Cronin – mBio

Animal experiments 

The beneficial effects of Gracilaria lemaneiformis polysaccharides on obesity and the gut microbiota in high fat diet-fed mice – X Sun – Journal of Functional Foods

Modifications in gut microbiota and fermentation metabolites in the hindgut of rats after the consumption of galactooligosaccharide glycated with a fish peptide – W Jin – Food & Function

Pumpkin polysaccharide modifies the gut microbiota during alleviation of type 2 diabetes in rats – G Liu – International Journal of Biological Macromolecules

Prebiotic mannan-oligosaccharides augment the hypoglycemic effects of metformin in correlation with modulating gut microbiota – J Zheng – Journal of Agricultural and Food Chemistry

Animal microbiome 

Bacterial diversity in the feces of dogs with CPV infection – Y Zheng – Microbial Pathogenesis

Diversity, structure and sources of bacterial communities in earthworm cocoons – M Aira – Scientific Reports

Deleterious interaction between honeybees (Apis mellifera) and its microsporidian intracellular parasite Nosema ceranae was mitigated by administrating either endogenous or allochthonous gut microbiota strains. – SE Khoury – Frontiers in Ecology and Evolution

Differential susceptibility of whitefly-associated bacteria to antibiotic as revealed by metagenomics analysis – Z-H Lv – Infection, Genetics and Evolution

Discovery of antimicrobial lipodepsipeptides produced by a Serratia sp. within mosquito microbiomes – J Ganley – ChemBioChem

Plant, root, and soil microbiome

Preprint: Small-scale soil microbial community heterogeneity linked to landforms on King George Island, maritime Antarctica – Y Zhang – bioRxiv

Not only priming: Soil microbiota may protect tomato from root pathogens – M Chialva – Plant Signaling & Behavior

Natural revegetation of a semiarid habitat alters taxonomic and functional diversity of soil microbial communities – Y Guo – Science of The Total Environment

Response of soil microbes to a reduction in phosphorus fertilizer in rice-wheat rotation paddy soils with varying soil P levels – Y Wang – Soil and Tillage Research

Beneath the canopy: Linking drought-induced forest die off and changes in soil properties –  A Gazol – Forest Ecology and Management

Defoliation intensity and elevated precipitation effects on microbiome and interactome depend on site type in northern mixed-grass prairie – B Ma – Soil Biology and Biochemistry

Review: The rhizosphere microbiome: Significance in rhizoremediation of polyaromatic hydrocarbon contaminated soil – R Kotoky – Journal of Environmental Management

Inferring pathogen dynamics from temporal count data: the emergence of Xylella fastidiosa in France is probably not recent – S Soubeyrand – New Phytologist

Taxonomic and functional responses of soil microbial communities to annual removal of aboveground plant biomass – X Guo – Frontiers in Microbiology

Microbial communities of polluted sub-surface marine sediments – V Catania – Marine Pollution Bulletin

Contrasting responses of bacterial and fungal communities to aggregate-size fractions and long-term fertilizations in soils of northeastern China – H Liao – Science of The Total Environment

Mycorrhizal Networks Facilitate Tree Communication, Learning, and Memory – SW Simard – Memory and Learning in Plants

Effects of plant neighborhood on arbuscular mycorrhizal fungal attributes in afforested zones – X Chen – Forest Ecology and Management

Metagenomic binning reveals versatile nutrient cycling and distinct adaptive features in alphaproteobacterial symbionts of marine sponges –  E Karimi – FEMS Microbiology Ecology

Water and extremophile microbiome

Non-Psychrophilic Methanogens Capable of Growth Following Long-Term Extreme Temperature Changes, with Application to Mars – RL Mickol – Microorganisms

Built environment 

Obtaining green energy from dry-thermophilic anaerobic co-digestion of municipal solid waste and biodiesel waste – S Zahedi – Biosystems Engineering

Assessment of Indoor Microbial Quality of Library’s Premise: Case of Central Library of the University of Yaoundé I – KG Landry – Open Journal of Preventive Medicine

Impacts of Glutaraldehyde on Microbial Community Structure and Degradation Potential in Streams Impacted by Hydraulic Fracturing – MF Campa – Environmental Science & Technology

Microbial community composition and methanogens’ biodiversity during a temperature shift in a methane fermentation chamber – A Banach – Environmental Technology

Food microbiology

Unravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms – VTT Ho – International Journal of Food Microbiology

Bacterial community of industrial raw sausage packaged in modified atmosphere throughout the shelf life – S Raimondi – International Journal of Food Microbiology

Purple lettuce (Lactuca sativa L.) attenuates metabolic disorders in diet induced obesity – Y Han – Journal of Functional Foods

Effects of carbon dioxide on metabolite production and bacterial communities during kimchi fermentation – DH Park – Microbiology & Fermentation Technology

 

Techniques

Metabolomics assisted metabolic network modeling and network wide analysis of metabolites in microbiology – J Wang – Critical Reviews in Biotechnology

Multi-omics approach identifies novel pathogen-derived prognostic biomarkers in patients with Pseudomonas aeruginosa bloodstream infection – M Willmann – bioRxiv

Review: Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies – CD Rudder –  Microbiome

5 – Analysis of Microbial Diversity: Regarding the (Paradoxical) Difficulty of Seeing Big in Metagenomics – C Vigliotti – Biodiversity and Evolution

Microbes in the news

You should probably clean your car’s interior NOW – Most germ-riddled areas REVEALED – Sunday Express

Drinking fermented probiotic beverage may lower blood pressure: Study – Deccan Chronicle

Investigation: Is the ‘five-second rule’ legitimate? – Philly Voice

Science, bacteria and recycled clothes at the Institute for Advanced Learning and Research – GoDanRiver

Beachful of bacteria – tgi

April 27, 2018

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Have a good Friday! Today’s Digest include a set of interesting reviews about the Hologenome concept, Clostridium difficile, the relation between microbiota and tuberculosis and microbiota transplantation. This digest also contains interesting articles about the use of dietary studies to control diet in microbiota studies, microbiome in cancer, microbiome and depression in rats and microbiome in soil from the Atacama’s desert.

 

Human and General Microbiome

Bile Acids and the Gut Microbiome as Potential Targets for NAFLD Treatment – Lixin Zhu – Journal of Pediatric Gastroenterology and Nutrition

Review: The role of fecal microbiota transplantation in inflammatory bowel disease – Irene D’Odorico – Journal of Digestive Diseases

Review: Put “gender glasses” on the effects of phenolic compounds on cardiovascular function and diseases – Ilaria Campesi – European Journal of Nutrition

Use of dietary indices to control for diet in human gut microbiota studies – Ruth C. E. Bowyer – Microbiome

Review: The hologenome concept of evolution after 10 years – Eugene Rosenberg – Microbiome

Pharmabiotic Manipulation of the Microbiota in Gastrointestinal Disorders: A Clinical Perspective – Fanny Giron – Journal of Neurogastroenterology and Motility

Microbiota potential for the treatment of sexual dysfunction – Hassan Tirandaz – Medical Hypotheses

Gut microbiome analysis identifies potential aetiological factors in acute gastroenteritis – Natalia Castaño-Rodríguez – Immunity and Infection

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Gut microbiome of Moroccan colorectal cancer patients – Imane Allali – Medical Microbiology and Immunology

Systematic Review: Safety and efficacy of encapsulated fecal microbiota transplantation for recurrent Clostridium difficile infection: a systematic review – Umair Iqbal – European Journal of Gastroenterology & Hepatology

Alterations in Enteric Virome Associate With Colorectal Cancer and Survival Outcomes – Geicho Nakatsu – Gastroenterology

High relative abundance of firmicutes and increased TNF-α levels correlate with obesity in children – Yaneth C Orbe-Orihuela – Salud Pública de México (Article in English)

Perspective: Why does the microbiome affect behaviour? – Katerina V.-A. Johnson – Nature Reviews Microbiology

Research Highlight: Exercise affects gut microbiota and bone – Claire Greenhill – Nature Reviews Endocrinology

Review: Clostridium difficile – From Colonization to Infection – Holger Schäffler – Frontiers in Microbiology

MiniReview: New Players in Immunity to Tuberculosis: The Host Microbiome, Lung Epithelium, and Innate Immune Cells – Nancy Gupta – Frontiers in Immunology

 

Animal Microbiome

A meta-barcoding approach to assess and compare the storage temperature-dependent bacterial diversity of gilt-head sea bream (Sparus aurata) originating from fish farms from two geographically distinct areas of Greece – Foteini F.Parlapani – International Journal of Food Microbiology

High-fat diet induces depression-like behaviour in mice associated with changes in microbiome, neuropeptide Y, and brain metabolome – Ahmed M. Hassan – Nutritional Neuroscience

Cascading effects on bacterial communities: cattle grazing causes a shift in the microbiome of a herbivorous caterpillar – Tali S. Berman – The ISME Journal

Microbiomes associated with bovine periodontitis and oral health – Ana C.Borsanelli – Veterinary Microbiology

Microbiota-accessible carbohydrates suppress Clostridium difficile infection in a murine model – Andrew J. Hryckowian – Nature Microbiology

High-Fat Diet Induces Dysbiosis of Gastric Microbiota Prior to Gut Microbiota in Association With Metabolic Disorders in Mice – Cong He – Frontiers in Microbiology

Differential Microbial Communities of Omnivorous and Herbivorous Cattle in Southern China – Susanna K.P.Lau – Computational and Structural Biotechnology Journal

 

Plant/Soil Microbes

A microorganisms’ journey between plant generations – Nathan Vannier – Microbiome

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health – Ioannis A. Stringlis – PNAS

Bacterial potentials for uptake, solubilization and mineralization of extracellular phosphorus in agricultural soils are highly stable under different fertilization regimes – Martin Grafe – Environmental Microbiology Reports

 

Extremophiles

Microbiome analysis and bacterial isolation from Lejía Lake soil in Atacama Desert – Dinka Mandakovic – Extremophiles

 

Beneficial Microbes and Compounds

Current and future uses of probiotics – Georgia Tanner – JAAPA

Barley β-glucan improves metabolic condition via short-chain fatty acids produced by gut microbial fermentation in high fat diet fed mice – Junki Miyamoto – PLoS One

Systematic Review: Are probiotic treatments useful on fibromyalgia syndrome or chronic fatigue syndrome patients? A systematic review – P. Roman – Beneficial Microbes

Review: The application of in vitro human intestinal models on the screening and development of pre- and probiotics – V.T. Pham – Beneficial Microbes

 

Antimicrobial Resistance

Acquisition of multidrug-resistant organisms in the absence of antimicrobial exposure – E M C D’Agata – Clinical Infectious Diseases

 

Food Microbiome

Variation in the Microbiome, Trichothecenes, and Aflatoxins in Stored Wheat Grains in Wuhan, China – Qing-Song Yuan – Toxins

 

Methodologies

Review: Single-cell metagenomics: challenges and applications – Yuan Xu – Protein & Cell

 

April 26, 2017

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General microbiome

Baseline urine metabolic phenotype in patients with severe alcoholic hepatitis and its association with outcome – Jaswinder Singh Maras – Hepatology communications

Checkpoint Checkmate: Microbiota Modulation of Cancer Immunotherapy – Eric C. Keen – Clinical chemistry

Metagenomics Analysis of Bacterial Population of Tympanosclerotic Plaques and Cholesteatomas – M. Tayyar Kalcioglu – Otolaryngology–Head and Neck Surgery

Drinking alcohol is associated with variation in the human oral microbiome in a large study of American adults – Xiaozhou Fan – Microbiome

Pregnancy and early life

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure – Cecilie Dahl – International Journal of Epidemiology

Gut microbial functional maturation and succession during human early life – Tomás Cerdó – Environmental microbiology

Human respiratory microbiome

Modelling upper respiratory tract diseases: getting grips on host-microbe interactions in chronic rhinosinusitis using in vitro technologies – Charlotte De Rudder Microbiome

Human skin microbiome

Skin microbiota and allergic symptoms associate with exposure to environmental microbes – Jenni Lehtimäki – PNAS

Human gut microbiome

Review :Dysbiosis in Functional Bowel Disorders – Paul Enck – Annals of Nutrition and Metabolism

Review: Inflammatory Bowel Disease and Immunonutrition: Novel Therapeutic Approaches Through Modulation of Diet and the Gut Microbiome – Larissa S Celiberto- Immunology

Comment : Richness and ecosystem development across faecal snapshots of the gut microbiota – Gwen Falony – Nature microbiology
Effects of gut microbiota manipulation on ex vivo lipolysis in human abdominal subcutaneous adipocytes – Johan W. E. Jocken – Adipocyte

Chronic kidney disease, uremic milieu, and its effects on gut bacterial microbiota dysbiosis – Lee D Chaves – American Journal of Physiology-Renal Physiology

Microbiota transplantation: concept, methodology and strategy for its modernization – Faming Zhang – Protein & Cell

The effects of sequencing platforms on phylogenetic resolution in 16 S rRNA gene profiling of human feces – Tae Woong Whon – Scientific Data

Gut Microbiota: From Microorganisms to Metabolic Organ Influencing Obesity – Richard W. Stephens – Obesity

Gut Microbes and Health: A Focus on the Mechanisms Linking Microbes, Obesity, and Related Disorders – Marialetizia Rastelli – Obesity

Review article: Impact of dietary gut microbial metabolites on the epigenome – Clarissa Gerhauser – Philosophical. Transactions of the Royal Society B

Animal experiments 

Gut Microbiota-Derived Tryptophan Metabolites Modulate Inflammatory Response in Hepatocytes and Macrophages – Cell Reports – Smitha Krishnan

Modulation of Active Gut Microbiota by Lactobacillus rhamnosus GG in a Diet Induced Obesity Murine Model – Yosep Ji – Frontiers in Microbiology

Lactobacilli Are Prominent Members of the Microbiota Involved in the Ruminal Digestion of Barley and Corn – Hee E. Yang

Intestinal microbiome of broiler chickens after use of nanoparticles and metal salts – Еlena Yausheva – Environmental Science and Pollution Research

Distinct consequences of amoxicillin and ertapenem exposure in the porcine gut microbiome – Sheila Connelly – Anaerobe

Indole, a Signaling Molecule Produced by the Gut Microbiota, Negatively Impacts Emotional Behaviors in Rats – Mathilde Jaglin – Frontiers in Neuroscience

Animal microbiome 

Microbiome of Total Versus Live Bacteria in the Gut of Rex Rabbits – Xiangchao Fu – Frontiers in Microbiology

Plant, root, and soil microbiome

Inferring Roles in Defense from Metabolic Allocation of Rice Diterpenoids – Xuan Lu – The Plant Cell

Genotypic variation in Pinus radiata responses to nitrogen source are related to changes in the root microbiome – Marta Gallart – FEMS Microbiology Ecology

Competition and habitat filtering jointly explain phylogenetic structure of soil bacterial communities across elevational gradient – Qian Zhang – Environmental Microbiology

Seagrass rhizosphere microenvironment alters plant‐associated microbial community composition – Kasper Elgetti Brodersen – Environmental Microbiology

Water and extremophile microbiome

Comparing Rock-inhabiting Microbial Communities in Different Rock Types from a High Arctic Polar Desert – Yong-Hoe Choe – FEMS Microbiology Ecology

Microbial communities in bakken region produced water – Daniel Lipus – FEMS Microbiology Letters

Aerobic microbial taxa dominate deep subsurface cores from the Alberta oil sands – Christina M Ridley – FEMS Microbiology Ecology

Metal contaminations impact archaeal community composition, abundance and function in remote alpine lakes – Sergi Compte‐Port – Environmental Microbiology

 Probiotics / prebiotics

Clinical and Microbiological Effect of a Multispecies Probiotic Supplementation in Celiac Patients With Persistent IBS-type Symptoms: A Randomized, Double-Blind, Placebo-controlled, Multicenter Trial – Ruggiero Francavilla – Journal of Clinical Gastroenterology

Review: Are Probiotics Effective in Targeting Alcoholic Liver Diseases? – Meegun Hong – Probiotics and Antimicrobial Proteins

April 25, 2018

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Method for cell-free transcription-translation to characterize nonmodel bacteria, a review of bile acid metabolism by the gut microbiota, altitude affects on the lizard intestinal microbiota.

Events and jobs

Research Applications Programmer – UC San Diego Center for Microbiome Innovation

Pregnancy and early life

Preterm infants have distinct microbiomes not explained by mode of delivery, breastfeeding duration or antibiotic exposure – Cecilie Dahl – International Journal of Epidemiology

Multi-site human microbiome

Bifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics – Aline C Freitas – PLOS ONE

Human skin microbiome

The Skin Commensal Yeast Malassezia globosa Thwarts Bacterial Biofilms to Benefit the Host – Giuseppe Ianiri – Journal of Investigative Dermatology

Human gut microbiome

A repeat offender: recurrent extraintestinal Clostridium difficile infection following fecal microbiota transplantation – Bradley J Gardiner – Anaerobe

Next-Generation Immune Repertoire Sequencing as a Clue to Elucidate the Landscape of Immune Modulation by Host–Gut Microbiome Interactions – Tatsuo Ichinohe – Frontiers in Immunology

Review: Metabolism of hydrogen gases and bile acids in the gut microbiome – Phillip B Hylemon – FEBS Letters

Animal experiments

Beneficial effects of a selected probiotic mixture administered to high fat-fed mice before and after the development of obesity – Marianna Roselli – Journal of Functional Foods

Emodin ameliorates ulcerative colitis by the flagellin-TLR5 dependent pathway in mice – Shuang Luo – International Immunopharmacology

Pre-print: Probiotics enhance susceptibility of mice to cryptosporidiosis – Bruno C M Oliveira – bioRxiv

Review: Using murine colitis models to analyze probiotics–host interactions – Rebeca Martín – FEMS Microbiology Reviews

Dietary Clostridium Butyricum induces a phased shift in fecal microbiota structure and increases the acetic acid-producing bacteria in a weaned piglet model – Jie Zhang – Journal of Agricultural and Food Chemistry

Animal microbiome

Changes in intestinal microbiota across an altitudinal gradient in the lizard Phrynocephalus vlangalii – Wenya Zhang – Ecology and Evolution

New York City House Mice (Mus musculus) as Potential Reservoirs for Pathogenic Bacteria and Antimicrobial Resistance Determinants – Simon H Williams – mBio

Glucocorticoids modulate gastrointestinal microbiome in a wild bird – José C Noguera – Royal Society Open Science

Plant, root, and soil microbiome

Insights to plant‐microbe interactions provide opportunities to improve resistance breeding against root diseases in grain legumes – Lukas Wille – Plant, Cell & Environment

Rice Phyllosphere Bacillus Species and Their Secreted Metabolites Suppress Aspergillus flavus Growth and Aflatoxin Production In Vitro and in Maize Seeds – Subbaiah Chalivendra – Toxins

Root diameter predicts the extramatrical hyphal exploration distance of the ectomycorrhizal fungal community – Weile Chen – Ecosphere

Isolation and characterization of phosphofungi, and screening of their plant growth-promoting activities – Xiaohui Wang – AMB Express

Plants regulate the effects of experimental warming on the soil microbial community in an alpine scrub ecosystem – Zhiliang Ma – PLOS ONE

Pre-print: Effects of fertilizations on soil bacteria and fungi communities in a degraded arid steppe revealed by high through-put sequencing – Luhua Yao – PeerJ

Water and extremophile microbiome

Life on the edge: active microbial communities in the Kryos MgCl2-brine basin at very low water activity – Lea Steinle – The ISME Journal

Light availability impacts structure and function of phototrophic stream biofilms across domains and trophic levels – Mia M Bengtsson – Molecular Ecology

Bacterial Community in Water and Air of Two Sub-Alpine Lakes in Taiwan – Kshitij Tandon – Microbes and Environments

Microbes in space

Book chapter: The Search for Signatures of Life and Habitability on Planets and Moons of Our Solar System – Oliver Funke – Biological, Physical and Technical Basis of Cell Engineering

Bioinformatics

Phylogenetic Placement of Exact Amplicon Sequences Improves Associations with Clinical Information – Stefan Janssen – mSystems

Pre-print: Fusobacterium genomics using MinION and Illumina sequencing enables genome completion and correction – S Michelle Todd – bioRxiv

Pre-print: FusoPortal: An interactive repository of hybrid MinION-sequenced Fusobacterium genomes improves gene identification and characterization – Blake E Sanders – bioRxiv

Comparison of normalization methods for the analysis of metagenomic gene abundance data – Mariana Buongermino Pereira – BMC Genomics

Pre-print: Accuracy of taxonomy prediction for 16S rRNA and fungal ITS sequences – Robert C Edgar – PeerJ

Pre-print: Natural history bycatch: a pipeline for identifying metagenomic sequences in RADseq data – Iris Holmes – PeerJ

Metabolomics

Exploring the Genetic Landscape of Metabolic Phenotypes with MetaboSignal – Andrea Rodriguez-Martinez – Current Protocols in Bioinformatics

Tissue Multiplatform-Based Metabolomics/Metabonomics for Enhanced Metabolome Coverage – Panagiotis A Vorkas – Metabolic Profiling

Review: Current and future perspectives of functional metabolomics in disease studies–A review – Min Yan – Analytica Chimica Acta

Techniques

Rapid acquisition and model-based analysis of cell-free transcription–translation reactions from nonmodel bacteria – Simon J Moore – PNAS

Pre-print: Impact of DNA sequencing and analysis methods on 16S rRNA gene bacterial community analysis in dairy products – Zhengyao Xue – bioRxiv

Methodological considerations for the identification of choline and carnitine-degrading bacteria in the gut – Eleanor Jameson – Methods

More microbes

Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms – Emilia Palazzotto – Current Opinion in Microbiology

Helicobacter pylori the Latent Human Pathogen or an Ancestral Commensal Organism – Jackie Li – Frontiers in Microbiology

Microbes in the news

Wiping out the gut microbiome could help with heart failure – ScienceDaily

How bacteria are changing your mood – James Gallagher – BBC News

Drinkers have more bad mouth bacteria, study finds – Susan Scutti – CNN

$11.2 million federal grant to support microorganism and disease research – EurekAlert

A Surprising Way Dogs Are Similar to Humans – Julissa Treviño – Smithsonian

Could Your Diet Be The Cause Of Your Arthritis Pain? – Robert Glatter – Forbes

Growing evidence that probiotics are good for your liver – ScienceDaily

Just being outside can improve your psychological health, and maybe your physical health too – Zoë Schlanger – Quartz

Role of Mosquito Microbiota in Reducing Malaria Transmission – JoAnna Pendergrass – American Veterinarian

A search for some of Earth’s most extreme creatures in the West Coast’s deepest underwater canyon – Amina Khan – Los Angeles Times

How plastic-eating bacteria actually work—a chemist explains – Emily Flashman – Phys.org

Far-red fluorescent silk can kill harmful bacteria as biomedical and environmental remedy – Kayla Wiles – Phys.org

Antibiotic-resistant bacteria cross oceans hidden in cargo ships – Inga Vesper – New Scientist

Fight against Zika, dengue get boost from reliable spread of bacteria – EurekAlert

Microbes on the market

Rebiotix Presents Posters at ECCMID 2018 Highlighting Microbiome Health Index™ Value Potential and RBX2660 Phase 2 Clinical Program Data – PR Newswire

Kaleido Biosciences Announces Appointment of Joshua Brumm as Chief Financial Officer – Citizen Tribune

Science, career, and publishing

Pre-print: Aligning interests: Integrating Citizen Science Efforts into Schools Through Service Requirements – Ginger Tsueng – bioRxiv

Randomly auditing research labs could be an affordable way to improve research quality: A simulation study – Adrian G Barnett – PLOS ONE