Category Archives: Events and jobs

May 12, 2018

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Today’s highlights in our Microbiology picks: Antibacterial activity of nested concentric patterns, relationship between the microbiota epitopes and antigenic epitopes, a book chapter on N-Acetyl transferase microbes, core microbiota for de novo IBD, soil microbes and disease suppression, fungi of office dust, microbes of potable  water from the Himalayan region, articles from ‘Techniques’ section.

Today’s highlights in our non-microbes picks: Epidemiology is important, recent on-goings on harassment, mental health awareness in academia, mimicking the prebiotic chemistry using flow chemistry, step taken by Wellcome Trust against misconduct in academia including harassment, Horizon 2020 budget for 2021-27.

 

Events and jobs

Laboratory Manager : New York, NY, United States – Albert Einstein College of Medicine – Deadline: 18 May 2018

General microbiome

Supramolecular Kandinsky circles with high antibacterial activity – H Wang – Nature Communications

Microbiota epitope similarity either dampens or enhances the immunogenicity of disease-associated antigenic epitopes – SC Pro – PLoS One

Genomic evolution of Staphylococcus aureus isolates colonizing the nares and progressing to bacteremia – JB Benoit – PLoS One

Book chapter: N-Acetyltransferases Microorganisms – S Boukouvala – Arylamine N-acetyltransferases in Health and Disease:From Pharmacogenetics to Drug Discovery and Diagnostics

 

Human vaginal microbiome

Preprint: Metatranscriptome analysis of the vaginal microbiota reveals potential mechanisms for protection against metronidazole in bacterial vaginosis – Z-L Deng – bioRxiv

Human gut microbiome

Preprint: Variability of core microbiota in newly diagnosed treatment-naïve paediatric Inflammatory Bowel Disease patients – TGJ de Meij – bioRxiv

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

Animal experiments 

Preprint: Bottlenecks in the transmission of Porcine reproductive and respiratory syndrome virus (PRRSV1) to naïve pigs and quasi-species variation during infection in partially immune pigs – M Cortey – bioRxiv

Lactobacillus gasseri PA-3 utilizes the purines GMP and guanosine and decreases their absorption in rats – N Yamada – Nucleosides, Nucleotides & Nucleic Acids

An exclusive metabolic niche enables strain engraftment in the gut microbiota – ES Sheperd – Nature

Interleukin 1α-Deficient Mice Have an Altered Gut Microbiota Leading to Protection from Dextran Sodium Sulfate-Induced Colitis – M Nunberg – mSystems

Animal microbiome 

Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing – F Zepeda-Paulo – PeerJ

Plant, root, and soil microbiome

Effect of land use and soil organic matter quality on the structure and function of microbial communities in pastoral soils: Implications for disease suppression – BEA Dignam – PLoS One

Relations between bacterial communities and enzyme functions of two paddy soils – X Luo – European Journal of Soil Science

Nematophagus fungi increasing phosphorus uptake and promoting plant growth – TSA Monteiro – Biological Control

Water and extremophile microbiome 

Effect of elevated pressure on ferric iron reduction coupled to sulfur oxidation by biomining microorganisms – R Zhang – Hydrometallurgy

Halophilic & halotolerant prokaryotes in humans – EH Seck – Future Medicine

Preprint: Structural variability and functional association in the epiphytic bacteria assemblies of freshwater macrophytes (Myriophyllum spicatum) – L Xian – bioRxiv

Investigation of nutrients and faecal coliforms removal in wastewater using a hydroponic system – SF Ndulini – Physics and Chemistry of the Earth, Parts A/B/C

Built environment 

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

 

Phages and viruses

Preprint: First report on Bacterial Diversity of Potable Spring water of Indian Himalayan Region – AK Singh – bioRxiv

Preprint: “In plaque-mass spectrometry imaging” reveals a major metabolic shift towards odd-chain fatty acid lipids induced by host-virus interactions – G Schleyer – bioRxiv

Preprint: Adventitious viruses persistently infect three commonly used mosquito cell lines – J Weger-Lucarelli – bioRxiv

Techniques

Preprint: High-resolution ISR amplicon sequencing reveals personalized oral microbiome – C Mukherjee – bioRxiv

Preprint: Transcriptome Analysis of Neisseria gonorrhoeae During Natural Infection Reveals Differential Expression of Antibiotic Resistance Determinants Between Men and Women – K Nudel – bioRxiv

Designer cells programming quorum-sensing interference with microbes – F Sedlmeyer – Nature Communications

A comprehensive model for assessment of liver stage therapies targeting Plasmodium vivax and Plasmodium falciparum – A Roth – Nature Communications

Preprint: Detection and quantification of the heterogeneity of S. aureus bacterial populations to identify antibiotic-induced persistence – MH Hasan – bioRxiv

Rapid isolation of fast-growing methanotrophs from environmental samples using continuous cultivation with gradually increased dilution rates – J Kim – Applied Microbiology and Biotechnology

Microbes in the news

Stanley Falkow, Who Saw How Bacteria Cause Disease, Dies at 84 – NY Times

How the Bugs In Your Gut Could Affect Your Blood Vessels – Live Science

Faeces transplant: The best cure for severe diarrhoea may be more faeces – Times Live

Cancer-killing viruses show promise — and draw billion-dollar investment – Nature

Does where we live affect our skin microbiome? – Medical News Bulletin

Non-Microbiology Picks

Editorial: Epidemiology is a science of high importance – Nature Communications

Mimicking the surface and prebiotic chemistry of early Earth using flow chemistry – DJ Ritson – Nature Communications

I’d whisper to my student self: you are not alone – D Reay – Nature

Harassment should count as scientific misconduct – E Marín-Spiotta – Nature

€100-billion budget proposed for Europe’s next big research programme – I Vesper – Nature

Editorial: The #MeToo campaign is gaining ground in China – Nature

Editorial: What to do to improve postgraduate mental health – Nature

Report harassment or risk losing funding, says top UK science funder – H Else – Nature

78,000-year-old record of Middle and Later stone age innovation in an East African tropical forest – C Shipton – Nature Communications

KACST Impact – Nature Communications

 

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 8, 2018

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Today’s Digest is again short and sweet. Human RNA interacts with oral commensals, viral communities diverge between different delivery modes, and Wash U researchers reveal how soil bacteria can digest antibiotics.Today’s Digest is again short and sweet. Human RNA interacts with oral commensals, viral communities diverge between different delivery modes, and Wash U researchers reveal how soil bacteria can digest antibiotics.

Jobs and Events

Microbial Sequencing and Analytics Core Director – Cleveland Clinic – Cleveland, OH, United States

Microbial Culturing and Engineering Core Director – Cleveland Clinic – Cleveland, OH, United States

Personalization and the microbiome in precision medicine: Probiota Americas 2018 program revealed – Stephen Daniells – NutraIngredients-USA

Pregnancy and early life

Preprint: The developing premature infant gut microbiome is a major factor shaping the microbiome of neonatal intensive care unit rooms – Brandon Brooks et al. – bioRxiv

Human oral microbiome

** Human tRNA-Derived Small RNAs Modulate Host–Oral Microbial Interactions – X He & F Li et al. – Journal of Dental Research

Press: UCLA researchers discover cellular messengers communicate with bacteria in the mouth – Brianna Aldrich – UCLA Newsroom

Animal experiments

Mouse: Frontline Science: Microbiota reconstitution restores intestinal integrity after cisplatin therapy – Alfredo Perales‐Puchalt & Jairo Perez‐Sanz et al. – Journal of Leukocyte Biology

Preprint: Antibiotic-induced dysbiosis predicts mortality in an animal model of Clostridium difficile infection – Charles Burdet et al. – bioRxiv

Water and extremophile microbiome

Screening of polyhydroxyalkanoate- producing bacteria and PhaC-encoding genes in two hypersaline microbial mats from Guerrero Negro, Baja California Sur, Mexico – Carolina A. Martı ́nez-Gutie ́rrez et al. – PeerJ

Phages and viruses
** Viromes of one year old infants reveal the impact of birth mode on microbiome diversity – Angela McCann, Feargal J. Ryan, & Stephen R. Stockdale et al. – PeerJ

Microbes in the news

Are the gut microbiota determined by genes or the environment? – C.I. Villamil – Medical News Bulletin

The Skin microbiota: a target for Next Generation active ingredients – M. Bey, E. Filaire and JY. Berthon – Premium Beauty News

AI Detects Patterns Of Gut Microbes for Cholera Risk – Marla Vacek Broadfoot – Duke Today

Catheter-associated Infections: Prevention using Polymers – Christine Kelly

Faecal bacteria found in coffee shop ice after random checks – BBC

** Wash U researchers reveal how some bacteria are able to eat antibiotics –  Shahla Farzan – St. Louis Public Radio

Superbugs: are we returning to an era where bacteria are a major killer without a cure? – Anthony McDonnell – LSE blogs

What does ape dung tell us about human health? Gut bacteria in primates’ faeces suggests we are deficient in fibre – Alexandra Thompson – Daily Mail

Vegan Kimchi Is Microbially Pretty Close to the Original – Marissa Fessenden – Smithsonian Mag

Calf gut health starts at birth – Jennifer Carrico – High Plains Journal

Microbes on the market

Amway signs R&D partnership – Rachel Watson – GRBJ

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

 

May 1, 2018

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A light Digest today with many bioRxiv articles and news pieces. The European Food Safety Authority warns about an emerging fungal pathogen for salamanders, heavy drinking doesn’t bode well for your oral microbiota, and a company is lifting the scientific bar for probiotics.

Jobs

Program Manager, Microbiology – Rutgers, The State University of New Jersey – Ewing, NJ

General microbiology

** Risk of survival, establishment and spread of Batrachochytrium salamandrivorans (Bsal) in the EU – EFSA Panel on Animal Health and Welfare et al. – EFSA Journal

Preprint: Identification of small regulatory RNAs involved in persister formation – Shanshan Zhang et al. – bioRxiv

Preprint: Identification of novel genes including rpmF and yjjQ critical for Type II persister formation in Escherichia coli – Shuang Liu et al. – bioRxiv

Pregnancy and early life

Preprint: Neonatal gut-microbiome-derived 12,13 DiHOME impedes tolerance and promotes childhood atopy and asthma – Sophia R Levan et al. – bioRxiv

Animal experiments

Preprint: Changes in the gut microbiota and fermentation products associated with enhanced longevity in acarbose-treated mice – Byron J. Smith et al. – bioRxiv

Animal microbiome

Preprint: To B or not to B: Arsenophonus as a source of B-vitamins in whiteflies – Diego Santos-Garcia et al. – bioRxiv

Plant, root and soil microbiome

Preprint: Diversity of Culturable Endophytic bacteria from Wild and Cultivated Rice showed potential Plant Growth Promoting activities – Madhusmita Borah et al. – bioRxiv

Water and extremophile microbiome

Exogenous acyl-homoserine lactones adjust community structures of bacteria and methanogens to ameliorate the performance of anaerobic granular sludge – Longyi Lv et al. – Journal of Hazardous Materials

Preprint: Parallel Evolution of Key Genomic Features and Cellular Bioenergetics Across the Marine Radiation of a Bacterial Phylum – Eric W Getz et al. – bioRxiv

Technology

Preprint: Genome Wide Identification Of Bacterial Genes Required For Plant Infection By Tn-Seq – Kevin Royet et al. – bioRxiv

Preprint: Longitudinal tracking of Plasmodium falciparum clones in complex infections by amplicon deep sequencing – Anita Lerch et al. – bioRxiv

Preprint: Diagnosis of Human Leptospirosis: High Resolution Melting Analysis for Direct Detection of Leptospira in the Early Stage of the Disease in a Clinical Setting – Lisa Marques Esteves et al. – bioRxiv

Microbes in the news

Does Gut Microbiota Manipulate Our Minds? – Sci-News

Pancreatic Cancer and the Microbiome — In the Clinic – C. Andrew Kistler – Cancer Therapy Advisor

University of Hohenheim to start microbiome research center – Feedstuffs

** Heavy drinking may increase ‘bad’ bacteria in your mouth, study finds – Jason Lemon – Atlanta Journal Constitution

Vapers and non-smokers have the same flourishing gut flora – Science Daily

Drink kills good bacteria, leaving you at the mercy of disease-causing ‘baddies’ – ELIZABETH MERAB – Healthy Nation

Clinical trial offers natural eczema treatment, using good bacteria to fight the bad – EurekAlert

Why some bacteria eat antibiotics and what we can do about it – Maggie Fox – NBC News

Mediterranean diet increases ‘good’ gut bacteria – Honor Whiteman – Medical News Today

Probiotics For Babies And Kids? New Research Explores Good Bacteria – Allison Aubrey – NPR

Microbes on the market

Evogene unit Biomica designs molecules to analyze bacteria – Gali Weinreb – Globes

** Seed could change the $50 billion probiotic market by relying on real science – Erin Brodwin – The Australian Financial Review

Scientific Communication

Preprint: High impact journals in ecology cover proportionally more statistically significant findings – Silvia Ceausu et al. – bioRxiv

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

April 19, 2018

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Today we have a few day’s worth of microbiome science to chew on… some interesting skin microbiome studies, bioinformatics publications, and our typical servings of gut /plant-root-soil/animal/water-extremophiles/general microbiome studies.  Dig in!

Events and jobs

Manager, QC Microbiology – Celgene – Phoenix, AZ

Pathology and Microbiology & IPID Graduate Student Research Seminar – UNMC

General microbiome

Cost-benefit analysis of introducing next-generation sequencing (metagenomic) pathogen testing in the setting of pyrexia of unknown origin – Jia Hui Chai – PLOS ONE

* [pre-print] Phylogenetically novel uncultured microbial cells dominate Earth microbiomes – Karen G. Lloyd – bioRxiv

Hologenomics: Systems-Level Host Biology – Kevin R. Theis – mSystems

Antibiotics as Instigators of Microbial Dysbiosis: Implications for Asthma and Allergy – Tomasz P. Wypych – Trends in Immunology

[perspective] Function and functional redundancy in microbial systems – Stilianos Louca – Nature Ecology & Evolution

Human oral microbiome

Comparison of the oral microbiome in mouthwash and whole saliva samples – Xiaozhou Fan – PLOS ONE

Oral Dysbiotic Communities and Their Implications in Systemic Diseases – Preethi Sudhakara – Dentistry Journal

Human skin microbiome

[pre-print] Umbilical Microbiome and Laparoscopic Surgery: A Descriptive Clinical Study – Aiolfi Alberto – Journal of Laparoendoscopic & Advanced Surgical Techniques

The skin microbiome of wound scars and unaffected skin in patients with moderate to severe burns in the subacute phase – Su‐Hsun Liu – Wound Repair and Regeneration

Human gut microbiome

Microbiome-Mediated Bile Acid Modification: Role in Intestinal Drug Absorption and Metabolism – Elaine F. Enright – Pharmacological Research

Non-microbicidal small molecule inhibition of polysaccharide metabolism in human gut microbes: a potential therapeutic avenue – Anthony D. Santilli – ACS Chemical Biology

The Use of Antimicrobials as Adjuvant Therapy for the Treatment of Obesity and Insulin Resistance: Effects and Associated Mechanisms – Sandra Aparecida dos Reis – Diabetes / Metabolism Research and Reviews

* Human Gut Microbiota Predicts Susceptibility to Vibrio cholerae Infection – Firas S Midani – The Journal of Infectious Disease

Interactions of Dihydromyricetin, a Flavonoid from Vine Tea (Ampelopsis grossedentata) with Gut Microbiota – Li Fan – Journal of Food Science

Characteristics of the gut microbiota in adult patients with type 1 and 2 diabetes based on the analysis of a fragment of 16S rRNA gene using next-generation sequencing – Dominika Salamon – Polish Archives of Internal Medicine

The Intestinal Microbiota in Colorectal Cancer -Herbert Tilg – Cancer Cell

The Endotoxemia Marker Lipopolysaccharide‐Binding Protein is Reduced in Overweight‐Obese Subjects Consuming Pomegranate Extract by Modulating the Gut Microbiota: A Randomized Clinical Trial – Antonio González‐Sarrías – Molecular Nutrition

Hepatocellular Carcinoma is Associated with Gut Microbiota Profile and Inflammation in Non-Alcoholic Fatty Liver Disease – Francesca Romana Ponziani – Hepatology

Antibiotic‐Associated Disruption of Microbiota Composition and Function in Cirrhosis is Restored by Fecal Transplant – Jasmohan S Bajaj – Hepatology

Does the gastrointestinal microbiome contribute to the “obesity paradox” in melanoma survival? – E A Langan – British Journal of Dermatology

Animal experiments

Obese Mice Losing Weight Due to trans-10,cis-12 Conjugated Linoleic Acid Supplementation or Food Restriction Harbor Distinct Gut Microbiota – Laura J den Hartigh – JN The Journal of Nutrition

Tuna oil alleviate D-galactose induced aging in mice accompanied by modulating gut microbiota and brain protein expression – Dijun Zhang – Journal of Agricultural and Food Chemistry

Dietary Mannan Oligosaccharides Modulate Gut Microbiota, Increase Fecal Bile Acid Excretion, and Decrease Plasma Cholesterol and Atherosclerosis Development – Lisa R. Hoving – Molecular Nutrition

[Review] The Role of the Gut Microbiota in the Metabolism of Polyphenols as Characterized by Gnotobiotic Mice – Pasinetti, Giulio Mari – Journal of Alzheimer’s Disease

Animal microbiome 

Shared larval rearing environment, sex, female size and genetic diversity shape Ae. albopictus bacterial microbiota – Guillaume Minard – PLOS ONE

Metatranscriptome analysis of the microbial fermentation of dietary milk proteins in the murine gut – Floor Hugenholtz – PLOS ONE

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

* Bacterial communities associated with honeybee food stores are correlated with land use – Philip Donkersley – Ecology and Evolution

Evaluating the microbiome of two sampling locations in the nasal cavity of cattle with bovine respiratory disease complex (BRDC) – Tara G McDaneld – Journal of Animal Science

Controlling ticks and tick-borne diseases…looking forward – José de la Fuente – Ticks and Tick-borne Diseases

The inside tract: The appendicular, cecal, and colonic microbiome of captive aye‐ayes – Lydia K. Greene – American Journal of Physical Anthropology

Water system is a controlling variable modulating bacterial diversity of gastrointestinal tract and performance in rainbow trout – Omolola C. Betiku – PLOS ONE

Comparative Analysis of the Microbiota Between Sheep Rumen and Rabbit Cecum Provides New Insight Into Their Differential Methane Production – Lan Mi – Frontiers in Microbiology

Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment – Geon Goo Han – Nature Scientific Reports

Development of the tonsillar microbiome in pigs from newborn through weaning – Luis Carlos Pena Cortes – BMC Microbiology

Plant, root, and soil microbiome

Antimicrobial peptide expression in a wild tobacco plant reveals the limits of host-microbe-manipulations in the field – Arne Weinhold – eLife

Identification of Major Rhizobacterial Taxa Affected by a Glyphosate-Tolerant Soybean Line via Shotgun Metagenomic Approach – Gui-Hua Lu – Genes

Culture‐independent analysis of hydrocarbonoclastic bacterial communities in environmental samples during oil‐bioremediation – Narjes Dashti – MicrobiologyOpen

Embracing Community Ecology in Plant Microbiome Research – Francisco Dini-Andreote – Trends in Plant Science

Cultivated bacterial diversity associated with the carnivorous plant Utricularia breviscapa (Lentibulariaceae) from floodplains in Brazil – Felipe Rezende Lima – Brazilian Journal of Microbiology

Soil microbial communities and glyphosate decay in soils with different herbicide application history – Keren Hernández Guijarro – Science of the Total Environment

Shining a light on the dark world of plant root-microbe interactions – Philip Poole – PNAS

Water and extremophile microbiome 

Microbial diversity and biomarker analysis of modern freshwater microbialites from Laguna Bacalar, Mexico – D. B. Johnson – gebiology

Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) – Zorigto Namsarae – Extremophiles

The ecology and diversity of microbial eukaryotes in geothermal springs – Angela M. Oliverio – The ISME Journal

Built environment

Deposition of Bacteria and Bacterial Spores by Bathroom Hot Air Hand Dryers – Luz del Carmen Huesca-Espitia – American Society for Microbiology

Food microbiology

Bacterial Communities in Serpa Cheese by Culture Dependent Techniques, 16S rRNA Gene Sequencing and High-throughput Sequencing Analysis – Maria Teresa P. Gonçalves – Journal of Food Science

Revealing the microbiota of marketed edible insects through PCR-DGGE, metagenomic sequencing and real-time PCR – Andrea Osimani – International Journal of Food Microbiology

Bioinformatics

Computer-guided design of optimal microbial consortia for immune system modulation – Richard R Stein – eLife

[uncorrected proof] Using pseudoalignment and base quality to accurately quantify microbial community composition – Mark Reppell – PLOS Computational Biology

Fast Metagenomic Binning via Hashing and Bayesian Clustering – Popic Victoria – Journal of Computational Biology

* Nonpareil 3: Fast Estimation of Metagenomic Coverage and Sequence Diversity – Luis M. Rodriguez-R – mSystems

Algorithms and strategies in short‐read shotgun metagenomic reconstruction of plant communities – Robert S. Harbert – Applications in Plant Science

Microbes in the news

Scientists Accidentally Make Plastic-Eating Bacteria Even More Efficient

New York City Mice: Here Are The Bacteria And Viruses That They Carry

Fecal microbiota transplant improves brain function in hepatic encephalopathy

Microbes on the market

Seres Therapeutics (MCRB) Presents New Preclinical Data Supporting the Development of Microbiome Therapeutics for Immuno-Oncology at AACR

Science, publishing, and career

Personal microbiome analysis improves student engagement and interest in Immunology, Molecular Biology, and Genomics undergraduate courses – K. Scott Weber – PLOS ONE

Ed’s non-microbiology picks

News articles below have actual study links inside.

Since 2016, Half of All Coral in the Great Barrier Reef Has Died

Marijuana’s effects on young brains diminish 72 hours after use, research says

Cannabinoids are easier on the brain than booze, study finds

Stem cell treatment drastically reduces drinking in alcoholic rats

The Ecology Of Disadvantage: Obesity Is Not Randomly Distributed Across The U.S., According To New Study

How your next meal could help fight depression, stress

Study: People with less political knowledge think they know a lot about politics

April 5, 2018

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Of note today: An evaluation of multi-site human microbiome temporal stability over six months; The impacts of 1,000 non-antibiotic drugs on the in vitro gut microbiome; Caspase-1 might modulate the relationship between stress, the gut microbiome, inflammation and depressive-like behaviour in mice; And the impact of warming on the Antarctic soil microbiome

Events and jobs

Community Sequencing Scientists, Indigo, Boston MA

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General microbiome

Review: No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases – Douglas B. Kell – Biological Review

Review: Environmental microbiology to the rescue of planet Earth – Víctor de Lorenzo – Environmental Microbiology

Multi-site human microbiome

*Quantification of Human Microbiome Stability over Six Months: Implications for Epidemiologic Studies – Rashmi Sinha – American Journal of Epidemiology

Review: Of genes and microbes: solving the intricacies in host genomes – Jun Wang – Protein & Cell

Human gut microbiome

Review: Serotonin as a Link Between the Gut-Brain-Microbiome Axis in Autism Spectrum Disorders – Narek Israelyan – Pharmacological Research

The Intestinal Microbiome Influences the Response of Cancers to PD-1–Based Immunotherapy: Might Fecal Transplantation Become Part of Cancer Therapy? – Paolo Biancheri – Gastroenterology

*Extensive impact of non-antibiotic drugs on human gut bacteria – Lisa Maier – Nature

Investigating Colonization of the Healthy Adult Gastrointestinal Tract by Fungi – Thomas A. Auchtung – mSphere

Vitamin D administration leads to a shift of the intestinal bacterial composition in Crohn’s Disease patients, but not in healthy controls – Holger Schäffler – Journal of Digestive Diseases

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Animal experiments

*The inflammasome and the microbiota-gut-brain axis – Ma-Li Wong – Neurology, Psychiatry and Brain Research

Exposure to Formaldehyde Perturbs the Mouse Gut Microbiome – Junhui Guo – Genes

Effect of prenatal administration of low dose antibiotics on gut microbiota and body fat composition of newborn mice – Ayumi Yoshimoto – Journal of Clinical Biochemistry and Nutrition

The Vibrio cholerae type VI secretion system can modulate host intestinal mechanics to displace gut bacterial symbionts – Savannah L. Logan – PNAS

Microbes vs. chemistry in the origin of the anaerobic gut lumen – Elliot S. Friedman – PNAS

Animal microbiome

Gastrointestinal microbial community changes in Atlantic cod (Gadus morhua) exposed to crude oil – Andrea Bagi – BMC Microbiology

Review: Host-microbe interactions in octocoral holobionts – recent advances and perspectives – Jeroen A. J. M. van de Water – BMC Microbiome

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Metatranscriptomics profile of the gill microbial community during Bathymodiolus azoricus aquarium acclimatization at atmospheric pressure – Inês Barros – AIMS Microbiology

Metagenomic analysis of bat guano samples revealed the presence of viruses potentially carried by insects, among others by Apis mellifera in Hungary – Zana Brigitta –  Acta Veterinaria Hungarica

Plant, root, and soil microbiome

Microbial community responses to modern environmental and past climatic conditions in Omongwa pan, western Kalahari: A paired 16S rRNA gene profiling and lipid biomarker approach – S. Genderjahn – Biogeosciences

Microbial communities inhabiting the fairy ring of Floccularia luteovirens and isolation of potential mycorrhiza helper bacteria – Rui Xing – Journal of Basic Microbiology

*Passive warming effect on soil microbial community and humic substance degradation in maritime Antarctic region – Dockyu Kim – Journal of Basic Microbiology

Effect of temperature on bacterial community in petroleum hydrocarbon-contaminated and uncontaminated Antarctic soil – C. W. Chong – Polar Biology

Variations of bacterial community diversity within the rhizosphere of three phylogenetically related perennial shrub plant species across environmental gradients – Xiaofan Na – Frontiers in Microbiology

Agromyces mangrovi sp. nov., a novel actinobacterium isolated from the rhizosphere of a mangrove – Moriyuki Hamada – Archives of Microbiology

Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam – C.N. Le – Biological Control

Microbial Decomposer Dynamics: Diversity and Functionality Investigated through a Transplantation Experiment in Boreal Forests – Alessia Bani – Microbial Ecology

Investigation of the core microbiome in main soil types from the East European plain – Elizaveta V. Pershina – Science of The Total Environment

Water and extremophile microbiome

Rare unclassified 16S rRNA operational taxonomic units from the uncharted Engaño Bay (Argentinean Patagonia) – Andrea Y. Calvo – Canadian Journal of Microbiology

Review: Extremophilic yeasts: the toughest yeasts around? – Pietro Buzzini – Yeast

Neptunicoccus sediminis gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from the Yellow Sea – Yan-Jiao Zhang – International Journal of Systematic and Evolutionary Microbiology

Responses of stream microbes to multiple anthropogenic stressors in a mesocosm study – Julia K. Nuy – Science of The Total Environment

*Evidence for selective bacterial community structuring on microplastics – Martin Ogonowski – Environmental Microbiology

Microbial Ecology

In vitro co-cultures of human gut bacterial species as predicted from co-occurrence network analysis – Promi Das – PLOSone

Review: What will it take to understand the ecology of symbiotic microorganisms? – Angela E Douglas – Environmental Microbiology

Built environment

Fungi-induced paint deterioration and air contamination in the Assiut University hospital, Egypt – Ismail R. Abdel-Rahim – Indoor and Buility Environment

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Probiotics / prebiotics

Lactobacilli and lactoferrin: Biotherapeutic effects for vaginal health – Lucia Bertuccini – Journal of Functional Foods

The viability of probiotics in water, breast milk, and infant formula – Claire Watkins – European Journal of Pediatrics

Bioinformatics

Constructing Lightweight And Flexible Pipelines Using Plugin-Based Microbiome Analysis (PluMA) – Trevor Cickovski – Bioinformatics

Numerical analyses of intestinal microbiota by data mining – Toshio Kobayashi – Journal of Clinical Biochemistry and Nutrition

Waste and Pollution

Low-dissolved-oxygen nitrification in tropical sewage: an investigation on potential, performance and functional microbial community – S. W. How – Water Science and Technology

Techniques

Visualization of Microbiota in Tick Guts by Whole-Mount In Situ Hybridization – Caitlin E. Moss – Jove

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Microbes in the news

Phage-host interactions are more complicated than most laboratory studies suggest – Phys.org

 

March 30, 2018

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In today’s digest you can read a perspective on the social network of microorganisms by Karsten Zengler, a paper on relationship between HIV-1 infection and chronic periodontitis by Tábata Larissa, a paper on sponges-cyanobacteria associations – a global diversity overview by Despoina Konstantinou and/or for an easier read check the report on bacteria in rubber duckies in our ‘News’ section. Enjoy!

Jobs

PhD position Ecology and Evolution of Microbial Infectious Ecosystems, University of Groningen, Groningen, Netherlands

Research Assistant-Post Doc, Karl Landsteiner University of Health Sciences, Krems, Austria

Post-doctoral opportunity at Weill Cornell in New York City, NY, USA

Post Doc Position for Genetic Engineering to Improve Microbial Soluble Expression, BOKU, Vienna, Austria

General microbiome

Perspective: The social network of microorganisms — how auxotrophies shape complex communities – Karsten Zengler – Nature Reviews Microbiology

Intracellular signaling through the comRS system in Streptococcus mutans genetic competence – Simon A.M. Underhill – bioRxiv

Ecological Insights from the Evolutionary History of Microbial Innovations – Mario E Muscarella – bioRxiv

Probing the metabolism of microorganisms – Stilianos Louca – Science

Human respiratory microbiome

Review: Streptococcus pneumoniae: transmission, colonization and invasion – Jeffrey N. Weiser – Nature Reviews Microbiology

Oral microbiome

Relationship between human immunodeficiency virus (HIV-1) infection and chronic periodontitis – Tábata Larissa – Expert Review of Clinical Immunology

Alterations in the oral microbiome in HIV-infected participants after ART administration are influenced by immune status –  Rachel M. Presti – AIDS

Human gut microbiome

A feasibility study: association between gut microbiota enterotype and antibody response to seasonal trivalent influenza vaccine in adults – Nick Shortt – Clinical and Translational Immunology

Gut microbiota varies by opioid use, circulating leptin and oxytocin in African American men with diabetes and high burden of chronic disease – Elena Barengolts – PLOS One

Variations in gut microbiota and fecal metabolic phenotype associated with Fenbendazole and Ivermectin Tablets by 16S rRNA gene sequencing and LC/MS-based metabolomics in Amur tiger – Fengping He – Biochemical and Biophysical Research Communications

Single Sampling Versus Multiple Testing Strategy to Assess Gut Microbiota Composition: Does It Matter? – T. G. J. de Meij – Current Microbiology

Scaling Safe Access to Fecal Microbiota Transplantation: Past, Present, and Future – Pratik Panchal – Current Gastroenterology Reports

Fecal Microbiome Among Nursing Home Residents with Advanced Dementia and Clostridium difficile – Rafael Araos – Digestive Diseases and Sciences

Intestinal Metagenomes and Metabolomes in Healthy Young Males: Inactivity and Hypoxia Generated Negative Physiological Symptoms Precede Microbial Dysbiosis – Robert Šket – Frontiers in  Physiology

Intestinal Microbiota Influences Non-intestinal Related Autoimmune Diseases – Maria C. Opazo – Frontiers in Microbiology

Third-party fecal microbiota transplantation following allo-HCT reconstitutes microbiome diversity – Zachariah DeFilipp – Blood Advances

Animal experiments 

Ecological Restoration of Antibiotic-Disturbed Gastrointestinal Microbiota in Foregut and Hindgut of Cows – Shoukun Ji – Frontiers in Cellular and Infection Microbiology

Effect of live yeast Saccharomyces cerevisiae (Actisaf Sc 47) supplementation on the performance and hindgut microbiota composition of weanling pigs – T. G. Kiros – Scientific Reports

Oral Antibiotic Treatment of Mice Exacerbates the Disease Severity of Multiple Flavivirus Infections – Larissa B. Thackray – Cell Reports

Animal microbiome 

Investigation of the seasonal microbiome of Anopheles coluzzii mosquitoes in Mali – Benjamin J. Krajacich – PLOS One

A Lethal Fungus Infects the Chinese White Wax Scale Insect and Causes Dramatic Changes in the Host Microbiota – Tao Sun – Scientific Reports

Widespread Elevational Occurrence of Antifungal Bacteria in Andean Amphibians Decimated by Disease: A Complex Role for Skin Symbionts in Defense Against Chytridiomycosis – Alessandro Catenazzi – Frontiers in Microbiology

Skin Microbiomes of California Terrestrial Salamanders Are Influenced by Habitat More Than Host Phylogeny – Alicia K. Bird – Frontiers in Microbiology

Plant, root, and soil microbiome

Insights into microbial communities mediating the bioremediation of hydrocarbon-contaminated soil from an Alpine former military site – José A. Siles – Applied Microbiology and Biotechnology

Endophytic bacterial microbiome associated with leaves of genetically modified (AtAREB1) and conventional (BR 16) soybean plants – Katiúscia Kelli Montanari-Coelho – World Journal of Microbiology and Biotechnology

Response of Nitrifier and Denitrifier Abundance and Microbial Community Structure to Experimental Warming in an Agricultural Ecosystem – Tatoba R. Waghmode – Frontiers in Microbiology

Bacterial diversity and community structure in the rhizosphere of four Ferula species – Xiuling Wang – Scientific Reports

Water and extremophile microbiome

Sponges-Cyanobacteria associations: Global diversity overview and new data from the Eastern Mediterranean – Despoina Konstantinou – PLOS One

Seasonal variation in the bacterial community composition of a large estuarine reservoir and response to cyanobacterial proliferation – Zheng Xu – Chemosphere

Assessment of Fecal Indicator Bacteria and Potential Pathogen Co-Occurrence at a Shellfish Growing Area – Andrew K. Leight – Frontiers in Microbiology

Diversity and Contributions to Nitrogen Cycling and Carbon Fixation of Soil Salinity Shaped Microbial Communities in Tarim Basin – Min Ren – Frontiers in Microbiology

Carrying Capacity and Colonization Dynamics of Curvibacter in the Hydra Host Habitat – Tanita Wein – Frontiers in Microbiology

Transcriptomic and Ectoine Analysis of Halotolerant Nocardiopsis gilva YIM 90087T Under Salt Stress – Jian Han –  Frontiers in Microbiology

Cultivation and genomics of the first freshwater SAR11 (LD12) isolate – Michael W. Henson – The ISME Journal

Metabolic Adaptation of Methanogens in Anaerobic Digesters Upon Trace Element Limitation – Babett Wintsche – Frontiers in Microbiology

Phages and viruses

Review: Autophagy during viral infection — a double-edged sword – Younho Choi – Nature Reviews Microbiology

Viruses in the environment – presence and diversity of bacteriophage and enteric virus populations in the Umhlangane River, Durban, South Africa – Veronna Marie – Journal of Water and Health

Kinetic Modeling of Virus Growth in Cells – John Yin – Microbiology and Molecular Biology Reviews

Bioinformatics

EzMap: a simple pipeline for reproducible analysis of the human virome – Patrick Czeczko  – Bioinformatics

Techniques

Reproducibility and repeatability of six high-throughput 16S rDNA sequencing protocols for microbiota profiling – Sajan C.Raju – Journal of Microbiological Methods

Mapping bacteria on filter membranes, an innovative SERS approach – SiyueGao – Journal of Microbiological Methods

Comparison of a newly developed binary typing with ribotyping and multilocus sequence typing methods for Clostridium difficile – Zhirong Li  – Journal of Microbiological Methods

Rapid detection of Klebsiella pneumoniae, Klebsiella oxytoca, Raoultella ornithinolytica and other related bacteria in food by lateral-flow test strip immunoassays – Tatsuya Tominaga –  Journal of Microbiological Methods

Detection of different classes of carbapenemases: Adaptation and assessment of a phenotypic method applied to Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii, and proposal of a new algorithm – Guillaume Gautier – Journal of Microbiological Methods

Rapid detection of carbapenemase-producing Acinetobacter baumannii and carbapenem-resistant Enterobacteriaceae using a bioluminescence-based phenotypic method – Vincent van Almsick – Journal of Microbiological Methods

A quest to find good primers for gene expression analysis of Candida albicans from clinical samples – Gabriela C.Alonso – Journal of Microbiological Methods

Microbes in the news 

The inside of rubber duckies are full of bacteria. You don’t seem surprised

Strings of electron-carrying proteins may hold the secret to ‘electric bacteria’

Researchers develop model to show how bacteria grow in plumbing systems

Harvard scientists uncover an exploitable Achilles’ heel common to most bacteria

Altering Gut Microbiome May Increase Resistance to C. difficile infection

Our Own Microbiome Might Be Triggering The Autoimmune Disease Lupus

March 29, 2018

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Of special note today: gut microbiota species expressing orthologs of human Ro60 might be involved in triggering and sustaining chronic autoimmunity in lupus; The portal vein blood microbiome in patients with liver cirrhosis; A randomized clinical study suggests dietary promotion of short chain fatty acid producing gut microbes as an effective treatment for type 2 diabetes; and the sexual dimorphism of root, flower and leaf microbiomes in the wild strawberry plant

Events and jobs

Clinical Laboratory Technologist IV (SL-1), Microbiology Laboratory – Stony Brook University – NY

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General microbiome

Review: Discovering antibiotics from the global microbiome – Yick Chong Lam – Nature Microbiology

Pregnancy and early life

Review: Milk Glycans and Their Interaction with the Infant-Gut Microbiota – Nina Kirmiz – Annual Review of Food Science and Technology

Multi-site human microbiome

*Commensal orthologs of the human autoantigen Ro60 as triggers of autoimmunity in lupus – Teri M. Greiling – Science Translational Medicine

Human nearly-sterile sites

*Circulating microbiome in blood of different circulatory compartments – Robert Schierwagen – BMJ Blood

Human gut microbiome

*Gut bacteria selectively promoted by dietary fibers alleviate type 2 diabetes – Liping Zhao – Science

Review: Impact of dietary compounds on cancer-related gut microbiota and microRNA – Muhammad Shahid Riaz Rajoka – Applied Microbiology and Biotechnology

Review: Influence of Altered Gut Microbiota Composition on Aging and Aging-Related Diseases – Jeonghyun Choi – Journal of Lifestyle Medicine

Review: Gut microbiome modulates efficacy of immune checkpoint inhibitors
Ming Yi – Journal of Hematology & Oncology

Protocol: Wisconsin microbiome study, a cross-sectional investigation of dietary fibre, microbiome composition and antibiotic-resistant organisms: rationale and methods  – Shoshannah Eggers – BMJ Journal

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Animal experiments

MicroRNA-146a Deficiency Protects against Listeria monocytogenes Infection by Modulating the Gut Microbiota – Chong-Tao Du – International Journal of Molecular Sciences

Loss of microRNA-21 Influences the Gut Microbiota Causing Reduced Susceptibility in a Murine Model of Colitis – Daniel G W Johnston – Journal of Crohn’s and Colitis

Towards an Integrative Understanding of tRNA Aminoacylation–Diet–Host–Gut Microbiome Interactions in Neurodegeneration – Elena L. Paley – Nutrients

Resilience of small intestinal beneficial bacteria to the toxicity of soybean oil fatty acids – Sara C Di Rienzi – eLife

Animal microbiome

Assessment of microbiome changes after rumen transfaunation: implications on improving feed efficiency in beef cattle – Mi Zhou – BMC Microbiology

Seasonal and algal diet-driven patterns of the digestive microbiota of the European abalone Haliotis tuberculata, a generalist marine herbivore – Angélique Gobet – BMC Microbiology

Diverse laboratory colonies of Aedes aegypti harbor the same adult midgut bacterial microbiome – Laura B. Dickson – BMC Parasites & Vectors

Plant, root, and soil microbiome

*The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – Scientific Reports

The potential of plant microbiota in reducing postharvest food loss – Franziska Buchholz – Microbial Biotechnology

Root microbiota shift in rice correlates with resident time in the field and developmental – Jingying Zhang – Science China Life Sciences

Microbial Ecology

Allometry and Ecology of the Bilaterian Gut Microbiome – Scott Sherrill-Mix – mBio

Preprint: Changes in the genetic requirements for microbial interactions with increasing community complexity – Manon Morin – bioRxiv

Built environment

Drinking water microbiome assembly induced by water stagnation – Fangqiong Ling – The ISME Journal

Food microbiology

Constraint-based modeling in microbial food biotechnology – Martin H. Rau – Biochemical Society Transactions

Characterization of microbial community structure and metabolic potential using Illumina MiSeq platform during the black garlic processing – Zhichang Qiu – Food Research International

Guidance on the characterisation of microorganisms used as feed additives or as production organisms – EFSA Panel on Additives and Products or Substances used in Animal Feed (FEEDAP) – EFSA Journal

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Probiotics / prebiotics

Probiotic treatment reduces the autistic-like excitation/inhibition imbalance in juvenile hamsters induced by orally administered propionic acid and clindamycin – Afaf El-Ansary – Metabolic Brain Disease

Review: A review of probiotic supplementation in healthy adults: helpful or hype? – Saman Khalesi – European Journal of Clinical Nutrition

Fecal Transplants

Effect of Vegan Fecal Microbiota Transplantation on Carnitine‐ and Choline‐Derived Trimethylamine‐N‐Oxide Production and Vascular Inflammation in Patients With Metabolic Syndrome – Loek P. Smits – Journal of the American Heart Association

Bioinformatics

Review: Exploring Linkages between Taxonomic and Functional Profiles of the Human Microbiome – Morgan G. I. Langille – mSystems

Techniques

Hybridization capture reveals microbial diversity missed using current profiling methods – Cyrielle Gasc – BMC Microbiology

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Microbes in the news

Just passing through: fungi not part of the gut – Fungus species don’t play a role in healthy human microbiomes – Andrew Masterson – Cosmos

Plants, fungi and bacteria work together to clean polluted land – Genetic analysis shows microbial interactions help fast-growing trees break down petrochemical pollutants in soil – Science Daily

Bacteria and Art

Art and biology students participate in creative collaboration – Sierra Guardiola – The Ithacan