Category Archives: Archaea

January 15, 2018

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Today’s digest is full of great papers, including new methods of detection and quantificaion of HGT in anoxic conditions, and a brilliant paper on root-rhizosphere interactome.

General Microbiome

Impact of the start-up process on the microbial communities in biocathodes for electrosynthesis. Mateos, R. Bioelectrochemistry.

Gut Microbiome

Dietary Factors Modulate Colonic Tumorigenesis Through the Interaction of Gut Microbiota and Host Chloride Channels. Zhang Y. Molecular Nutrition Food Research

Metagenomic and metabolomic analyses unveil dysbiosis of gut microbiota in chronic heart failure patients. Cui, X. Scientific Reports

Nasal Microbiome

An insight into intestinal mucosal microbiota disruption after stroke.Stanley,D. Scientific Reports

Influence of pig farming on the human’s nasal microbiota: The key role of the airborne microbial communities. Kraemer, JG. Applied and Environmental Microbiology

Fecal Microbiome

Letters to Editor: Sucrase-isomaltase 15Phe IBS risk variant in relation to dietary carbohydrates and faecal microbiota composition. Thingholm L. Gut

Plant, Soil, and Water Microbiome

Soil contamination alters the willow root and rhizosphere metatranscriptome and the root-rhizosphere interactome. Yergeau, E. The ISME Journal

Indoor Microbiome

Microbiomes in Dishwashers: Analysis of the microbial diversity and putative opportunistic pathogens in dishwasher biofilm communities.Raghupathi, PK. Applied and Environmental Microbiology

Resitome

Characteristics of ARG-carrying plasmidome in the cultivable microbial community from wastewater treatment system under high oxytetracycline concentration. Shi, Y. Applied Microbioloby and Biotechnology

Animan Experiments and Microbiome

Characterizing the bacterial microbiota in different gastrointestinal tract segments of the Bactrian camel. He, J. Scientific Reports

Effect of atorvastatin on the gut microbiota of high fat diet-induced hypercholesterolemic rats. Khan, TJ. Scientific Reports

Protocol/Techniques

Fluorescence recovery allows the implementation of a fluorescence reporter gene platform applicable for the detection and quantification of horizontal gene transfer in anoxic environments. Pinilla, R. Applied and Environmental Microbiology

Microbiome Jobs

Part-Time Microbiology Laboratory Technician

-Inside Higher Ed Careers

January 5, 2018

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Today’s digest has an interesting commentary on the oral-gut connection and a brilliant piece on microbial diversity. Lastly, a look at how grapevines influence belowground diversity and networks

General Microbiome

A role for the endometrial microbiome in dysfunctional menstrual bleeding. Pelzer ES. Antonie Van Leeuwenhoek.

Performance and microbial community variations of anaerobic digesters under increasing tetracycline concentrations. Xiong Y. Applied Microbiology and Biotechnology

In Nature, There Is Only Diversity. McLaren MR. MBio.

Gut Microbiome

Commentary: Oral-gut connection: one step closer to an integrated view of the gastrointestinal tract? Lira-Junior R. Mucosal Immunology

Bile acids at the cross-roads of gut microbiome-host cardiometabolic interactions. Ryan PM. Diabeticology and Metabolic Syndrome

REVIEW: Diet, Microbiota, and Metabolic Health: Trade-Off Between Saccharolytic and Proteolytic Fermentation. Korpela K. Annual of Food Science and Technology

Nasal and Lung Microbiome

REVIEW: Fungi in Bronchiectasis: A Concise Review. Máiz L. Internatioanal Journal of Molecular Sciences

Alterations in the mucosa-associated fungal microbiota in patients with ulcerative colitis. Qiu X. Oncotarget

The association between anterior nares and nasopharyngeal microbiota in infants hospitalized for bronchiolitis. Luna PN. Microbiome

Fecal Microbiome

Editorial Comment: Fecal microbiota transplantation as a possible treatment of irritable bowel syndrome. Juncadella AC. Annals of Translational Medicine

Plant, Soil, and Water Microbiome

Co-variation between Distribution of Microbial Communities and Biological Metabolization of Organics in Urban Sewer Systems. Jin P. Environmental Science and Technology.

Do invasive plants structure microbial communities to accelerate decomposition in intermountain grasslands? McTee MR. Ecology and Evolution

Grapevine rootstocks shape underground bacterial microbiome and networking but not potential functionality. Marasco R. Microbiome

Biodiversity of the microbial mat of the Garga hot spring. Rozanov AS. BMC Evolutionary Biology

Animal Experiments and Microbiome

Microbiota Reconstitution Does Not Cause Bone Loss in Germ-Free Mice. Quach D. mSphere

Physiological Translocation of Lactic Acid Bacteria during Pregnancy Contributes to the Composition of the Milk Microbiota in Mice. de Andrés J. Nutrients

Extreme sensitivity to ultraviolet light in the fungal pathogen causing white-nose syndrome of bats. Palmer JM. Nature Communication

OCCURRENCE OF PASTEURELLACEAE BACTERIA IN THE ORAL CAVITY OF SELECTED MARSUPIAL SPECIES. Hansen MJ. Journal of Zoo and Wildlife Medicine

Marine Microbiome

Agelas Wasting Syndrome Alters Prokaryotic Symbiont Communities of the Caribbean Brown Tube Sponge, Agelas tubulata.Deignan LK. Microbial Ecology

Environmental drivers of heterogeneity in the trophic-functional structure of protozoan communities during an annual cycle in a coastal ecosystem. Xu G. Marine Pollution Bulletin

Antibiotic Resitance

Editorial: Empiric antibiotic use in allogeneic hematopoietic cell transplantation: should we avoid anaerobe coverage? Shono Y. Blood Advances

Characterization of genetic determinants involved in antibiotic resistance in Aeromonas spp. and fecal coliforms isolated from different aquatic environments. Carnelli A. Research in Microbiology

 

 

December 11, 2017

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Today’s digest is quiet a treat- A microbiome survey of emergency medical service personnel (EMS), a Python release of Mothur, and a global recall of baby formula over contamination scares ( Lactalis )

General Microbiome

 The Emergency Medical Service Microbiome. Hudson AJ. Applied Environmental Microbiology

 Human Gut Microbiome

Towards utilization of the human genome and microbiome for personalized nutrition. Bashiardes S. Current Opinions in Biotechnology

Gut microbial profile analysis by MiSeq sequencing of pancreatic carcinoma patients in China. Ren Z. Oncotarget.

Lung Microbiome

The distal airway microbiome after lung transplantation: A driver of immune regulation? Mitchell AB. Journal of Heart and Lung Transplant

Plant, water, and soil microbiome

 Microbial communities in natural rubber coagula during maturation: impacts on technological properties of dry natural rubber. Salomez M. Journal of Applied Microbiology

Microbial ecology of the Agaricus bisporus mushroom cropping process.McGee CF. Applied Microbiology and Biotechnology

A new niche for anoxygenic phototrophs as endoliths. Roush D. Applied Environmental Microbiology

Animal experiments and microbiome

Co-occurrence of early gut colonization in neonatal piglets with microbiota in the maternal and surrounding delivery environments.Chen X. Anaerobe.

Techniques/Protocol

Metabolic Model Reconstruction and Analysis of an Artificial Microbial Ecosystem. Ye C. Methods in Molecular Biology

mothur-py 0.3.0

-PyPI

Microbes in the NEWS

‘Extremophile’ Antarctic Bacteria Could Unlock Secret to Alien Life (VIDEO)

-Sputnik International

French baby-milk maker Lactalis orders major product recall over bacteria fears

-Prothom Alo (English)

 

 

 

November 30, 2017

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A wide variety of interesting articles: Antibiotics administrated during labour impact  infant gut microbiome development, altered gut microbiome is related to liver function in individuals with Hep B, specific pathogens can alter social signaling in drosophila, a comphrensive study of the impact of diet on the lemur gut microbiome, a survey of antibiotic resistence genes in the drinking water across multiple continents, the impact of the hospital microbiome on the gut microbiome of preterm infants, the first evidence of a gut archeae impact on the host immune system, and two popular news articles refuting yesterday’s report of possible alien bacteria on the international space station.

Events and jobs

Web Developer, Microbiome Core – Harvard T.H. Chan School of Public Health

Account Manager – Microbiology –  South East England

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General microbiome

  • Health Economics and Regulations 

Faecal microbiota transplantation: a regulatory hurdle? – Frederick Verbeke – BMC Gastroenterology

Cost-effectiveness analysis of fecal microbiota transplantation for inflammatory bowel disease – Ting Zhang – Oncotarget

Pregnancy and early life

*Intrapartum antibiotics for GBS prophylaxis alter colonization patterns in the early infant gut microbiome of low risk infants – Jennifer C. Stearns – Scientific Reports

Human skin microbiome

Skin Immune Landscape: Inside and Outside the Organism – Florence Abdallah – Mediators of Inflammation

Human gut microbiome
*Gut Microbial Dysbiosis Is Associated with Altered Hepatic Functions and Serum Metabolites in Chronic Hepatitis B Patients – Jing Wang – Frontiers in Microbiology

Faecal bacterial microbiota in patients with cirrhosis and the effect of lactulose administration – Aditya Narayan Sarangi – BMC Gastroenterology

Delivered Fecal Microbiota Transplantation on Recurrent Clostridium difficile Infection – Dina Kao – JAMA

Capsules for Fecal Microbiota Transplantation in Recurrent Clostridium difficile Infection – Krishna Rao – JAMA

Review: Antibiotic therapy in neonates and impact on gut microbiota and antibiotic resistance development: a systematic review – Jon Widding Fjalstad – Journal of Antimicrobial Chemotherapy

Long-term proton pump inhibitor therapy leads to small bowel bacterial overgrowth as determined by breath hydrogen and methane excretion – Agnieszka Sieczkowska – Journal of Breath Research

Review: Impact of gut microbiota on drug metabolism: an update for safe and effective use of drugs – Keumhan Noh – Archives of Pharmacal Research

Evaluating the effect of Clostridium difficile conditioned medium on fecal microbiota community structure – Sabina Horvat – Scientific Reports

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Animal experiments

Preprint: The Vibrio cholerae Type VI Secretion System Can Modulate Host Intestinal Mechanics to Displace Commensal Gut Bacteria – Savannah L Logan – bioRxiv

Genes and Gut Bacteria Involved in Luminal Butyrate Reduction Caused by Diet and Loperamide – Nakwon Hwang – Genes

Simultaneous delivery of antibiotics neomycin and ampicillin in drinking water inhibits fermentation of resistant starch in rats – Diana G. Carvajal-Aldaz – Molecular Nutrition and Food Research

Animal microbiome

*Pathogenic bacteria enhance dispersal through alteration of Drosophila social communication – Ian W. Keesey – Nature Communications

*Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs – E. A. McKenney – Gut Microbes

Impact of Dietary Galacto-Oligosaccharide (GOS) on Chicken’s Gut Microbiota, Mucosal Gene Expression, and Salmonella Colonization – Rebecca-Ayme Hughes – Frontiers in Veterinary Science

Dietary energy drives the dynamic response of bovine rumen viral communities – Christopher L. Anderson – Microbiome

Effect of microalgae on intestinal inflammation triggered by soybean meal and bacterial infection in zebrafish – Karina Bravo-Tello – PLOS ONE

In vivo effects of Allium cepa L. on the selected gut microflora and intestinal histomorphology in broiler – Sajidur Rahman – Acta Histochemica

Enteric Pathogens and Their Toxin-Induced Disruption of the Intestinal Barrier through Alteration of Tight Junctions in Chickens – Wageha A. Awad – Toxins

Plant, root, and soil microbiome

The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria – Olaf Tyc – Trends in Microbiology

Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog – Max Reumer – Applied and Environmental Microbiology

Burkholderia humptydooensis sp. nov., a New Species Related to Burkholderia thailandensis and the Fifth Member of the Burkholderia pseudomallei Complex – Apichai Tuanyok – Applied and Environment Microbiology

Water and extremophile microbiome
Functional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications – Sekar Jinendiran – Probiotics and Antimicrobial Proteins

Resistome

Preprint: Increased usage of antiseptics is associated with reduced susceptibility in clinical isolates of S. aureus – Katherine Hardy – bioRxiv

*Catalogue of antibiotic resistome and host-tracking in drinking water deciphered by a large scale survey – Liping Ma – Microbiome

Review: Assessing the Risk of Antibiotic Resistance Transmission from the Environment to Humans: Non-Direct Proportionality between Abundance and Risk – Célia M. Manaia – Trends in Microbiology

Built environment

*Strain-resolved analysis of hospital rooms and infants reveals overlap between the human and room microbiome – Brandon Brooks – Nature Communications

Predominance and Metabolic Potential of Halanaerobium spp. in Produced Water from Hydraulically Fractured Marcellus Shale Wells – Daniel Lipus – Applied and Environment Microbiology

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Microbial Ecology

Effect of Antimicrobial and Physical Treatments on Growth of Multispecies Staphylococcal Biofilms – Elizabeth J. Stewart – Applied and Environment Microbiology

More Microbes

  • Archaea

*Associated Archaeon Methanosphaera stadtmanae Is Recognized through Its RNA and Induces – Tim Vierbuchen – Frontiers in Immunology

  • Synthetic Microbes

Analysis and Implementation of a Multicellular Feedback Control Strategy in a Synthetic Bacterial Consortium – Gianfranco Fiore – ACS Synthetic Biology

Techniques

Diazotroph community characterization via a high-throughput nifH amplicon sequencing and analysis pipeline – John Christian Gaby – Applied and Environmental Microbiology

Direct PCR Offers a Fast and Reliable Alternative to Conventional DNA Isolation Methods for Gut Microbiomes – Elin Videvall – mSystems

Generation of bacteriophage-insensitive mutants of Streptococcus thermophilus using an antisense RNA CRISPR-Cas silencing approach – Brian McDonnell – Applied and Environmental Microbiology

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Microbes in the news

*Bacteria on Space Station Likely From Germy Humans, Not Aliens – Elaina Zachos – National Geographic

*We are basically positive that the Russians did not find alien bacteria in space – Mary Beth Griggs – Popular Science

Custom Bacteria Make New Molecules On Demand – Sam Lemonick – Forbes

Toilet art sheds light on gut health – Newshub

November 28, 2017

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Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv

November 23, 2017

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Today we have pretty much diverse Microbiome Digest particularly in the section of General microbiome. Interesting papers on E coli as a model organism for metabolic engineering, influence of exercise on our gut microbiota and influence of antibiotics on genetic diversity of honeybee gut microbiota. Enjoy reading these and many many more articles and news about microbes.

Events and jobs

PhD in Soil Microbiology, Teagasc Johnstown Castle, UK

PhD Fellowship in Molecular Microbiology, Copenhagen, Denmark

Postdoctoral Research Associate – Bacterial Evolutionary Genomics, Missoula, MT, US

Postdoctoral researchers – (Lemon Lab), Cambridge MA, US

Associate Professor/Professor in Microbiology, Nottingham, UK

General microbiome

The Immunomodulatory Drug Glatiramer Acetate is Also an Effective Antimicrobial Agent that Kills Gram-negative Bacteria – Stig Hill Christiansen – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition – Xiang-Yi Li – bioRxiv

Complete Genome Sequences of Seven Vibrio cholerae Phages Isolated in China – Sudhakar G. Bhandare – Genome Announcements

Survival of microbes in Earth’s stratosphere – Priya Das Sarma – Current Opinion in Microbiology

Review: Cable Bacteria Take a New Breath Using Long-Distance Electricity – Filip J.R. Meysman – Trends in Microbiology

Characterization of the CrbS/R Two-Component System in Pseudomonas fluorescens Reveals a New Set of Genes under Its Control and a DNA Motif Required for CrbR-Mediated Transcriptional Activation – Edgardo Sepulveda – Frontiers in Microbiology

The effect of the 2015 Earthquake on the bacterial community compositions in water in Nepal – Sital R. Uprety – Frontiers in Microbiology

Rokubacteria: genomic giants among the uncultured bacterial phyla – Eric D. Becraft – Frontiers in Microbiology

A communal catalogue reveals Earth’s multiscale microbial diversity – Luke R. Thompson – Nature

Pregnancy and early life

Microbial Mechanistic Insight into the Role of Inulin in Improving Maternal Health in a Pregnant Sow Model – Pan Zhou – Frontiers in Microbiology

Human respiratory microbiome

A practical molecular identification of nonfermenting Gram-negative bacteria from cystic fibrosis – Carolina Paulino da CostaCapizzani – Brazilian Journal of Microbiology

Oral microbiome

Over-the-counter mouthwash use and risk of pre-diabetes/diabetes – Kaumudi J.Joshipura – Nitric Oxide

Profiling of Oral Microbiota in Early Childhood Caries Using Single-Molecule Real-Time Sequencing – Yuan Wang – Frontiers in Microbiology

Exploring the association between Alzheimer’s disease, oral health, microbial endocrinology and nutrition – Alice Harding – Frontiers in Aging Neuroscience

Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet – Florent Lassalle – Molecular Ecology

Human skin microbiome

Evaluation of short exposure times of antimicrobial wound solutions against microbial biofilms: from in vitro to in vivo – K Johani – Journal of Antimicrobial Chemotherapy

Human gut microbiome

Review: Influence of microbiota on intestinal immune system in ulcerative colitis and its intervention – Sailong Zhang – Frontiers in Immunology

Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans – Allen, Jacob M – Medicine & Science in Sports & Exercise

The Kynurenine Pathway As a Novel Link between Allergy and the Gut Microbiome – Aaron P. Van der Leek – Frontiers in Immunology

The gut microbiota: A new potential driving force in liver cirrhosis and hepatocellular carcinoma – Marco Sanduzzi Zamparelli – United European Gastroenterology Journal

Animal experiments 

Aged Gut Microbiota Contributes to Systemical Inflammaging after Transfer to Germ-Free Mice – Floris Fransen – Frontiers in Immunology

Animal microbiome

Species-specific signatures of the microbiome from Camponotus and Colobopsis ants across developmental stages – Manuela Oliveira Ramalho – PLOS One

Spontaneous body contractions are modulated by the microbiome of Hydra – Andrea P. Murillo-Rincon – Sceintific Reports

Age-related differences in the respiratory microbiota of chickens – Laura Glendinning – PLOS One

A potential new species of porcine Actinobacillus defined by multi-locus sequence analysis – C. Turni – Animal Production Science

Prevalence survey of Toxoplasma gondii in hearts from Western Australian sows – K. Hodgson – Animal Production Science

Antibiotics reduce genetic diversity of core species in the honeybee gut microbiome – Kasie Raymann –  Molecular Ecology

Plant, root, and soil microbiome

Rhizosphere Microbiome Recruited from a Suppressive Compost Improves Plant Fitness and Increases Protection against Vascular Wilt Pathogens of Tomato – Anastasis Antoniou – Frontiers in Plant Science

Exogenous nitrogen addition reduces the temperature sensitivity of microbial respiration without altering the microbial community composition – Hui Wei – Frontiers in Microbiology

Parallelized, aerobic, single carbon-source enrichments from different natural environments contain divergent microbial communities – Theodore M. Flynn – Frontiers in Microbiology

The effect of Lobelia dortmanna L. on the structure and bacterial activity of the rhizosphere – KatarzynaLewicka-Rataj – Aquatic Botany

Illumina-Based Analysis of Endophytic and Rhizosphere Bacterial Diversity of the Coastal Halophyte Messerschmidia sibirica – Xue-Ying Tian – Frontiers in Microbiology

Functionality of Root-Associated Bacteria along a Salt Marsh Primary Succession – Miao Wang – Frontiers in Microbiology

An Integrated Insight into the Relationship between Soil Microbial Community and Tobacco Bacterial Wilt Disease – Hongwu Yang – Frontiers in Microbiology

Water and extremophile microbiome

Deep ocean prokaryotic communities are remarkably malleable when facing long-term starvation – Marta Sebastián – Environmental Microbiology

Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods – Alexis L. Pasulka – Environmental Microbiology

Increased Denitrification Rates Associated with Shifts in Prokaryotic Community Composition Caused by Varying Hydrologic Connectivity – Abigail Tomasek – Frontiers in Microbiology

Chapter 4.1 – The Biota of Intermittent Rivers and Ephemeral Streams: Prokaryotes, Fungi, and Protozoans – Anna M. Romaní – Intermittent Rivers and Ephemeral Streams

Fungal diversity in deep-sea sediments of a hydrothermal vent system in the Southwest Indian Ridge – Wei Xu – Deep Sea Research Part I

Environmental factors shape water microbial community structure and function in shrimp cultural enclosure ecosystems – Dongwei Hou – Frontiers in Microbiology

Taxonomic and Functional Differences between Microbial Communities in Qinghai Lake and Its Input Streams – Ze Ren – Frontiers in Microbiology

Microbial Diversity and Community Structure of Sulfate-Reducing and Sulfur-Oxidizing Bacteria in Sediment Cores from the East China Sea – Yu Zhang – Frontiers in Microbiology
Stratified Bacterial and Archaeal Community in Mangrove and Intertidal Wetland Mudflats Revealed by High Throughput 16S rRNA Gene Sequencing – Zhichao Zhou – Frontiers in Microbiology

 

Food microbiology

Novel insights into microbial community dynamics during the fermentation of Central European ice wine – Mária Bučková – International Journal of Food Microbiology

Diversity within Italian Cheesemaking Brine-Associated Bacterial Communities Evidenced by Massive Parallel 16S rRNA Gene Tag Sequencing – Marilena Marino – Frontiers in Microbiology

Probiotics / prebiotics

Lactobacillus acidophilus Metabolizes Dietary Plant Glucosides and Externalizes Their Bioactive Phytochemicals – Mia C. Theilmann – mBio

Phages and viruses

Bacteriophage Transcytosis Provides a Mechanism To Cross Epithelial Cell Layers – Sophie Nguyen – mBio

MVP: a microbe–phage interaction database  – Na L. Gao – Nucleic Acids Research

Biotechnology

Enrichment of lignocellulose-degrading microbial communities from natural and engineered methanogenic environments – Emine Gozde Ozbayram – Applied Microbiology and Biotechnology

Escherichia coli as a model organism for systems metabolic engineering – Paul A.Adamczyk – Current Opinion in System Biology

Bioinformatics

Review: Computational Approaches for Integrative Analysis of the Metabolome and Microbiome – Jasmine Chong – Metabolites

Techniques

Nucleic acid purification from plants, animals and microbes in under 30 seconds – Yiping Zou – PLOS Biology

Lighting Van Leeuwenhoek’s samples – Lesley A. Robertson – FEMS Microbiology Letters

Analysis of Microbiome Data in the Presence of Excess Zeros – Abhishek Kaul – Frontiers in Microbiology

Stripping flow cytometry: How many detectors do we need for bacterial identification? – Peter Rubbens – Cytometry

Microbes in the news 

Plague Bacteria Entered Europe During Neolithic Age, Genetic Analysis Finds 

How the Immune System Identifies Invading Bacteria

Scientists Program Remote-Controlled Nanobots to Kill Cancer

Microbes on the market 

Qualitative Report on Human Microbiome Market 

Microbes and art

Superbugs And Rockets Side By Side At Science Museum

 

 

 

November 15, 2017

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Virome analysis of bats and archaea, bioinformatics tools for metatranscriptomics analysis, using mass spectrometry for studying microbiome metabolomics.

General microbiome

Review: An integrative omics perspective for the analysis of chemical signals in ecological interactions – A E Brunetti – Chemical Society Reviews

Pregnancy and early life

Pre-print: Hospitalized premature infants are colonized by related bacterial strains with distinct proteomic profiles – Christopher T Brown – bioRxiv

Human respiratory microbiome

The role of the microbiome in childhood asthma – Giovanna Pisi – Immunotherapy

Human vaginal microbiome

Pre-print: A new sequencing-based women’s health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth M Bik – bioRxiv

Human gut microbiome

Gut microbiota and body composition in anorexia nervosa inpatients in comparison to athletes, overweight, obese, and normal weight controls – Sabrina Mörkl – International Journal of Eating Disorders

Review: Gut Microbiota-Dependent Modulation of Energy Metabolism – C N Heiss – Journal of Innate Immunity

Animal experiments

Antimicrobial emulsifier – glycerol monolaurate induces metabolic syndrome, gut microbiota dysbiosis and systemic low-grade inflammation in low-fat diet fed mice – Zengliang Jiang – Molecular Nutrition and Food Research

A temperature sensitive Mycobacterium paragordonae induces enhanced protective immune responses against mycobacterial infections in the mouse model – Byoung-Jun Kim – Scientific Reports

Animal microbiome

Review: The B vitamin nutrition of insects: the contributions of diet, microbiome and horizontally acquired genes – Angela E Douglas – Current Opinion in Insect Science

Plant, root, and soil microbiome

Brassica napus has a key role in the recovery of the health of soils contaminated with metals and diesel by rhizoremediation – Rafael G Lacalle – Science of the Total Environment

Water and extremophile microbiome

Purification of eutrophic water containing chlorpyrifos by aquatic plants and its effects on planktonic bacteria – Xing-Jian Xu – Chemosphere

Cultivation of an immobilized (hyper)thermophilic marine microbial community in a bioreactor – M Landreau – FEMS Microbiology Letters

Pre-print: Dynamics of finely resolved, abundant symbiotic marine plankton and other interacting microbes via automated high-frequency sampling – David M Needham – bioRxiv

Food microbiology

Pre-print: Fusicatenibacter Is Associated with Kefir Drinking – Richard Sprague – bioRxiv

Probiotics/prebiotics

A novel double-layer mucoadhesive tablet containing probiotic strain for vaginal administration: Design, development and technological evaluation – María Teresa Sánchez – European Journal of Pharmaceutical Sciences

Efficacy and Safety of a Multistrain Probiotic Formulation Depends from Manufacturing – Vito Trinchieri – Frontiers in Immunology

Phages and viruses

Virome analysis of two sympatric bat species (Desmodus rotundus and Molossus molossus) in French Guiana – Arielle Salmier – PLOS ONE

Review: The enigmatic archaeal virosphere – David Prangishvili – Nature Reviews Microbiology

Bioinformatics

Old meets new: most probable number validation of metagenomic and metatranscriptomic datasets in soil – Tim H Mauchline – Letters in Applied Microbiology

Pre-print: AQMM: Enabling Absolute Quantification of Metagenome and Metatranscriptome – Xiao-Tao Jiang – bioRxiv

Metabolomics

Review: Mass spectrometry-based metabolomics: Targeting the crosstalk between gut microbiota and brain in neurodegenerative disorders – Hemi Luan – Mass Spectrometry Reviews

Pre-print: Coupling MALDI-TOF mass spectrometry protein and specialized metabolite analyses to rapidly discriminate bacterial function – Chase Clark – bioRxiv

Techniques

Evaluating in vitro culture medium of gut microbiome with orthogonal experimental design and metaproteomics approach – Leyuan Li – Journal of Proteome Research

More microbes

Pre-print: Chemotaxis allows bacteria to overcome host-generated reactive oxygen species that constrain gland colonization – Kieran D Collins – bioRxiv

Microbes in the news

Specimens of Earth’s Oldest Known Life Forms Have Been Discovered in Tasmania – Michelle Starr – Science Alert

Shape-shifting agent targets harmful bacteria in the stomach – Phys.Org

Opinion: Not Just Antibiotics: Is Cancer Chemotherapy Driving Antimicrobial Resistance? – Lito E Papanicolas – Trends in Microbiology

Microbes on the market

A Silicon Valley Startup Wants Women To Test Their Vaginal Microbiota At Home – Ellie Kincaid – Forbes

Seres teams with cancer heavyweights for microbiome-checkpoint inhibitor combination trial – Nick Paul Taylor – FierceBiotech

November 9, 2017

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Today, we have interesting papers about diet and microbiota both in human and other mammals. We have also papers about urchin and black slug microbiota and gut remediation (use of probiotics to manage metal accumulation).

 

Human Microbiome

State of the art: Manipulating the microbiome: evolution of a strategy to prevent S. aureus disease in children – D F Khamash – Journal of Perinatology

Clinical Parameters and Gut Microbiome Changes Before and After Surgery in Thoracic Aortic Dissection in Patients with Gastrointestinal Complications – Shuai Zheng – Scientific Reports

Distinct Campylobacter fetus lineages adapted as livestock pathogens and human pathobionts in the intestinal microbiota – Gregorio Iraola – Nature Communications

Impact of Lactobacillus reuteri colonization on gut microbiota, inflammation, and crying time in infant colic – Monica L. Nation – Scientific Reports

Outlook: Microbiome: A bag of surprises – Claire Ainsworth – Nature

Research Highlight: Gut microbiota: Oral bacteria: a cause of IBD? – Iain Dickson – Nature Reviews Gastroenterology and Hepatology

Commentary: Different Substrate Preferences Help Closely Related Bacteria To Coexist in the Gut – Petra Louis – mBio

Opinion: How poverty affects diet to shape the microbiota and chronic disease – Christy A. Harrison – Nature Reviews Immunology

Review: Balancing Herbal Medicine and Functional Food for Prevention and Treatment of Cardiometabolic Diseases through Modulating Gut Microbiota – Ming Lyu – Frontiers in Microbiology

Variation of Carbohydrate-Active Enzyme Patterns in the Gut Microbiota of Italian Healthy Subjects and Type 2 Diabetes Patients – Matteo Soverini – Frontiers in Microbiology

 

Animal Microbiome

Effect of Dietary Forage to Concentrate Ratios on Dynamic Profile Changes and Interactions of Ruminal Microbiota and Metabolites in Holstein Heifers – Jun Zhang –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Antibiotic-induced Alterations in Gut Microbiota are Associated with Changes in Glucose Metabolism in Healthy Mice – Richard R. Rodrigues – Frontiers in Microbiology

Phylogeny and Antagonistic Activities of Culturable Bacteria Associated with the Gut Microbiota of the Sea Urchin (Paracentrotus lividus) – Marinella Silva Laport – Current Microbiology

Dietary Uncoupling of Gut Microbiota and Energy Harvesting from Obesity and Glucose Tolerance in Mice – Matthew J. Dalby – Cell Reports

Metagenomic Analysis of the Gut Microbiome of the Common Black Slug Arion ater in Search of Novel Lignocellulose Degrading Enzymes – Ryan Joynson – Frontiers in Microbiology

Community structure of the metabolically active rumen bacterial and archaeal communities of dairy cows over the transition period – Zhigang Zhu – PLoS ONE

Intermittent Fasting Promotes White Adipose Browning and Decreases Obesity by Shaping the Gut Microbiota – Guolin Li – Cell Metabolism

Nonalcoholic Fatty Liver Disease Is Exacerbated in High-Fat Diet-Fed Gnotobiotic Mice by Colonization with the Gut Microbiota from Patients with Nonalcoholic Steatohepatitis – Chien-Chao Chiu – Nutrients

 

Beneficial Microbes and Molecules

Gut remediation: a potential approach to reducing chromium accumulation using Lactobacillus plantarum TW1-1 – Gaofeng Wu – Scientific Reports

(Provisionally accepted, Full text available soon) Lactobacillus plantarum MYS6 ameliorates fumonisin B1-induced hepatorenal damage in broilers – B V. Deepthi –  Frontiers in Microbiology

(Provisionally accepted, Full text available soon) Wuji Wan formula ameliorates diarrhoea and disordered colonic motility in post-inflammation irritable bowel syndrome rats by modulating the gut microbiota – Ying Chen – Frontiers in Microbiology

Polysaccharides from Chrysanthemum morifolium Ramat ameliorate colitis rats by modulating the intestinal microbiota community – Jin-Hua Tao – Oncotarget

 

Environmental Microbiology

Fungal Community Structure and As-Resistant Fungi in a Decommissioned Gold Mine Site – Silvia Crognale – Frontiers in Microbiology

 

Methods

Evaluation of the accuracy and sensitivity of high‑throughput sequencing technology using known microbiota – Fanjing Meng – Molecular Medicine Reports

 

October 20, 2017

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A wide variety of studies today from the digestive microbiota of carnivorous pitcher plants, to the skin microbiome of dogs, and the impacts of probiotics on male fertility in a mouse model of obesity. 

Events and jobs

Microbiome World Congress – November 7-8, 2017, Capital Hilton, Washington, DC – registration

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  • General microbiome

The Pelagic Bacterium Paraphotobacterium marinum Has the Smallest Complete Genome Within the Family Vibrionaceae – Zhaobin Huang – Frontiers in Microbiology

Review: Uncultivated microbes in need of their own taxonomy – Konstantinos T Konstantinidis – The ISME Journal

Review: The growing tree of Archaea: new perspectives on their diversity, evolution and ecology – Panagiotis S Adam – The ISME Journal

  • Human respiratory microbiome

Antibiotic exposure and interpersonal variance mask the effect of ivacaftor on respiratory microbiota composition – Anton Y. Peleg – Journal of Cystic Fibrosis

  • Human gut microbiome

Carbapenem-resistant Enterobacteriaceae colonization (CRE) and subsequent risk of infection and 90-day mortality in critically ill patients, an observational study – Thomas Howe McConville – PLOSone

Review: Antibiotics, gut microbiome, and obesity – Karen S. W. Leong – Clinical Endocrinology

Review: Gut microbiota changes in the extreme decades of human life: a focus on centenarians – Aurelia Santoro – Cellular and Molecular Life Sciences

Review: Salmonella enterica Serovar Typhimurium Strategies for Host Adaptation – Christopher J. Anderson – Frontiers in Microbiology

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  • Animal Experiments

Lactobacillus rhamnosus PB01 (DSM 14870) supplementation affects markers of sperm kinematic parameters in a diet-induced obesity mice model – Fereshteh Dardmeh – PLOSone

  • Animal microbiome

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization – Beate M Slaby – The ISME Journal

A polyphenol-enriched diet and Ascaris suum infection modulate mucosal immune responses and gut microbiota composition in pigs – Andrew R. Williams – PLOSone

Individual signatures and environmental factors shape skin microbiota in healthy dogs – Anna Cuscó – Microbiome

Review: Metagenomic investigation of gastrointestinal microbiome in cattle – Minseok Kim – AJAS

  • Plant, root, and soil microbiome

Linking the development and functioning of a carnivorous pitcher plant’s microbial digestive community – David W Armitage – The ISME Journal

Biogeography and organic matter removal shape long-term effects of timber harvesting on forest soil microbial communities – Roland C Wilhelm – The ISME Journal

Differences in soil fungal assemblages associated with native and non-native tree species of varying weediness – David R. Toole – Biological Invasions

Nitric Oxide Accumulation: The Evolutionary Trigger for Phytopathogenesis – Margarida M. Santana – Frontiers in Microbiology

  • Water and extremophile microbiome

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

Mixotrophy drives niche expansion of verrucomicrobial methanotrophs – Carlo R Carere – The ISME Journal

High abundance and expression of transposases in bacteria from the Baltic Sea – Theoden Vigil-Stenman – The ISME Journal

Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms – Kevin Anthony Meyer – PLOSone

High-throughput sequencing revealed novel Dehalococcoidia in dechlorinating microbial enrichments from PCB contaminated marine sediments – B. Matturro – FEMS Microbiology Ecology

Flooding Duration Affects the Structure of Terrestrial and Aquatic Microbial Eukaryotic Communities – Oliver Röhl – Environmental Microbiology

Sediment microbial taxonomic and functional diversity in a natural salinity gradient challenge Remane’s “species minimum” concept – Christina Pavloudi – PeerJ

The Exometabolome of Two Model Strains of the Roseobacter Group: A Marketplace of Microbial Metabolites – Gerrit Wienhausen – Frontiers in Microbiology

  • Built environment

Indoor microbiota in severely moisture damaged homes and the impact of interventions – Balamuralikrishna Jayaprakash – Microbiome

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  • Probiotics / prebiotics

Review: Probiotics in the Prevention of Gestational Diabetes Mellitus – Luisa F. Gomez Arango – Nutrition and Diet in Maternal Diabetes

  • Phages and viruses

Microencapsulation of Clostridium difficile specific bacteriophages using microfluidic glass capillary devices for colon delivery using pH triggered release – Gurinder K. Vinner – PLOSone

Novel chaperonins are prevalent in the virioplankton and demonstrate links to viral biology and ecology – Rachel L Marine – The ISME Journal

  • Techniques

A simpler and more cost-effective peptide biosynthetic method using the truncated GST as carrier for epitope mapping – Wan-Xiang Xu – PLOSone

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October 4, 2017

Posted on by

Today’s digest features excellent reviews on recent advances in cryo-electron microscopy technology for understanding bacterial ribosome assembly,  and impact of gut microbiome on therapeutics. Happy reading!

General microbiome

Towards standards for human fecal sample processing in metagenomic studies – Paul I Costea – Nature Biotechnology

Assessment of variation in microbial community amplicon sequencing by the Microbiome Quality Control (MBQC) project consortium – Rashmi Sinha – Nature Biotechnology

Editorial : Microbiome yarns: microbiome basis of memory – Kenneth Timmis – Microbial Biotechnology

Review : Cross Talk: The Microbiota and Neurodevelopmental Disorders – John R. Kelly – Frontiers in Neuroscience

Review : Gut Microbiota, Immune System, and Bone – P. D’Amelio – Calcified Tissue International

Pregnancy and early life

Meconium microbiome as a new source of information about long-term health and disease: questions and answers – P. Wilczyńska – The Journal of Maternal-Fetal & Neonatal Medicine

Evolution in fecal bacterial/viral composition in infants of two central African countries (Gabon and Republic of the Congo) during their first month of life – Lionel Brazier – Plos one

A longitudinal study of the infant nasopharyngeal microbiota: The effects of age, illness and antibiotic use in a cohort of South East Asian children – Susannah J. Salter – Plos one

Human gut microbiome

Review : Microbiota in digestive cancers: our new partner? – Anthony Lopez – Carcinogenesis

*Review : Impacts of the Human Gut Microbiome on Therapeutics – Yoshiki Vázquez-Baeza – Annual Reviews

Associations between acute gastrointestinal GvHD and the baseline gut microbiota of allogeneic hematopoietic stem cell transplant recipients and donors – C Liu – Leukemia

Natural polyreactive IgA antibodies coat the intestinal microbiota – Jeffrey J. Bunker – Science

Time of day and eating behaviors are associated with the composition and function of the human gastrointestinal microbiota – Jennifer L Kaczmarek – The American Journal of Clinical Nutrition

The Effects of an Environmentally Relevant Level of Arsenic on the Gut Microbiome and its Functional Metagenome – Liang Chi – Toxicological Sciences

Animal experiments

Probiotics modulate gut microbiota and improve insulin sensitivity in DIO mice – Renata A.Bagarolli – The Journal of Nutritional Biochemistry

Decaffeinated green and black tea polyphenols decrease weight gain and alter microbiome populations and function in diet-induced obese mice – Susanne M. Henning – European Journal of Nutritional

Microbiota-related Changes in Bile Acid & Tryptophan Metabolism are Associated with Gastrointestinal Dysfunction in a Mouse Model of Autism – Anna V. Golubeva – EBioMedicine

Repeated Oral Exposure to Nε-Carboxymethyllysine, a Maillard Reaction Product, Alleviates Gut Microbiota Dysbiosis in Colitic Mice – Nesreen ALJahdali – Digestive Disease Sciences

Comparison of the Luminal and Mucosa-Associated Microbiota in the Colon of Pigs with and without Swine Dysentery – Eric R. Burrough – Frontiers in Veterinary Science

Animal microbiome

Untangling the cecal microbiota of feral chickens by culturomic and metagenomic analyses – Chiara Ferrario – Environmental Microbiology

Bacterial community associated with worker honeybees (Apis mellifera) affected by European foulbrood – Tomas Erban – PeerJ

Comparative characterization of bacterial communities in geese fed all-grass or high-grain diets – Qi Xu – Plos One

Plant, root, and soil microbiome

Implication of graphene oxide in Cd-contaminated soil: A case study of bacterial communities – TingXiong – Journal of Environmental Management

Elucidating the microbial community associated with the protein preference of sludge degrading worms – Steef de Valk – Environmental Technology

Bacterial microbiomes of individual ectomycorrhizal Pinus sylvestris roots are shaped by soil horizon and differentially sensitive to nitrogen addition – Srisailam Marupakula – Environmental Microbiology

A comparative study of composting the solid fraction of dairy manure with or without bulking material: performance and microbial community dynamics – Xiao-ZhongZhong -Bioresource Technology

Water and extremophile microbiome

Individual-level trait diversity predicts phytoplankton community properties better than species richness or evenness – Simone Fontana – The ISME Journal

Bacterial community dynamics within an aerobic granular sludge reactor treating wastewater loaded with pharmaceuticals – Catarina L.Amorim – Ecotoxicology and Environmental Safety

Food Microbiology

Chlorogenic acid versus amaranth’s caffeoylisocitric acid – Gut microbial degradation of caffeic acid derivatives – Maren Vollmer – Food Research International

Probiotics / prebiotics

Specific signatures of the gut microbiota and increased levels of butyrate in children treated with fermented cow’s milk containing heat-killed Lactobacillus paracasei CBA L74 – Roberto Berni Canani – Applied and Environmental Microbiology

Beneficial effects of a probiotic blend on gastrointestinal side effects induced by leflunomide and amlodipine in a rat model – S.C. Song – Beneficial Microbes

Phages and viruses

Characterization of the human DNA gut virome across populations with different subsistence strategies and geographical origin – Simone Rampelli – Environmental Microbiology

Metabolomics

Identification of phenolic metabolites in human urine after the intake of a functional food made from grape extract by a high resolution LTQ-Orbitrap-MS approach – Gemma Sasot – Food Research International
http://www.sciencedirect.com/science/article/pii/S0963996917300297?via%3Dihub

Bioinformatics

A broken promise: microbiome differential abundance methods do not control the false discovery rate – Stijn Hawinkel – Briefings in Bioinformatics
https://academic.oup.com/bib/article/doi/10.1093/bib/bbx104/4091293/A-broken-promise-microbiome-differential-abundance

Metagenomic assembly through the lens of validation: recent advances in assessing and improving the quality of genomes assembled from metagenomes – Nathan D. Olson – Briefings in Bioinformatics

Ananke: temporal clustering reveals ecological dynamics of microbial communities – Michael W. Hall – PeerJ

Detection of Increased Plasma Interleukin-6 Levels and Prevalence of Prevotella copri and Bacteroides vulgatus in the Feces of Type 2 Diabetes Patients – Aline Zazeri Leite – Frontiers in Immunology

k-SLAM: accurate and ultra-fast taxonomic classification and gene identification for large metagenomic data sets – David Ainsworth – Nucleic Acids Research

Techniques

* The impact of recent improvements in cryo-electron microscopy technology on the understanding of bacterial ribosome assembly – Aida Razi – Nucleic acids Research

Anitha’s non-microbiology picks

A cold, clear view of life wins chemistry Nobel

Nobel physics prize awards discovery in gravitational waves

Medicine Nobel Prize Goes to Circadian Rhythm Researchers

New portable blood analyzer could improve anemia detection worldwide

Computational study sheds doubt on latest theory of birds’ mysterious magnetic compass