Category Archives: Techniques

May 5, 2018

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For the Saturday digest the theses on making pipelines of microbial communities available and microbes of butterflies; plus the whole section of animal microbiome would be my choice for reading.

General microbiome

Thesis: Making Pipelines and Large Processing Microbial Community Studies Available to Any User, Any Time, Any Place – JAN Molina – ProQuest

Multi-site human microbiome

Social networks, cooperative breeding, and the human milk microbiome – CL Meehan  – American Journal of Human Biology

 

Human gut microbiome

Fecal Microbiota Composition Drives Immune Activation in HIV-infected Individuals – CP Neff – EBioMedicine

Animal microbiome 

Thesis: Evolution of Microbial Communities and Chemosensory Genes in Passion-Vine Butterflies – B van Schooten – ProQuest

Microbial community and diversity in the feces of Sichuan takin (Budorcas taxicolor tibetana) as revealed by Illumina Miseq sequencing and quantitative real-time PCR – H Zhu – AMB Express

Comparison of the fecal microbiota of domestic commercial meat, laboratory, companion, and shelter rabbits (Oryctolagus cuniculi) – J Kylie – BMC Veterinary Research

Plant, root, and soil microbiome

Diversity of Bacillus-like bacterial community in the rhizospheric and non-rhizospheric soil of halophytes (Salsola stocksii and Atriplex amnicola) and characterization of osmoregulatory genes in halophilic Bacilli – S Mukhtar – Canadian Journal of Microbiology

Contrasting beneficial and pathogenic microbial communities across consecutive cropping fields of greenhouse strawberry – Y Huang – Applied Microbiology and Biotechnology

Reanalysis of microbiomes in soils affected by apple replant disease (ARD): Old foes and novel suspects lead to the proposal of extended model of disease development – L Nicola – Applied Soil Ecology

Root–Microbe Interactions: Understanding and Exploitation of Microbiome – A Sharma – Root Biology

Biodegradation of pyraclostrobin by two microbial communities from Hawaiian soils and metabolic mechanism – X Chen – Journal of Hazardous Materials

Water and extremophile microbiome 

Prokaryotic and eukaryotic community structure affected by the presence of an acid mine drainage from an abandoned gold mine – JO Bonilla – Extremophiles

 

Techniques

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation – Q Zeng – Microbiome

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

Taxonomic profiles in metagenomic analyses of free-living microbial communities in the Ofunato Bay – MS Reza – Gene

 

 

May 3, 2018

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

Human Microbiome and General

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

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

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

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

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

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

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

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

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

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

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

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

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

 

Animal Microbiome

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

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

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

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

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

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

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

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

 

Built Environments

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

 

Bioinformatics and Genomics

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

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

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

 

Plant/Soil Microbiomes

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

 

Other (Microbiome-related)

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

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

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

 

May 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 29, 2018

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

General microbiome

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

Multi-site human microbiome

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

Human respiratory microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

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

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

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

Animal experiments 

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

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

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

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

Animal microbiome 

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

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

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

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

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

Plant, root, and soil microbiome

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Water and extremophile microbiome

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

Built environment 

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

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

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

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

Food microbiology

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

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

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

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

 

Techniques

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

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

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

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

Microbes in the news

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

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

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

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

Beachful of bacteria – tgi

April 28, 2018

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Genomic analysis of tick endosymbionts, re-evaluation of the phylogenetic placement of mitochondria outside alphaproteobacteria, gravity sensing in fungi acquired by horizontal gene transfer from bacteria.

General microbiome

Review: Malaria and the microbiome: a systematic review – Matthew M Ippolito – Clinical Infectious Diseases

Pregnancy and early life

The fallopian tube microbiome: implications for reproductive health – Elise S Pelzer – Oncotarget

Animal microbiome

The influence of diet and environment on the gut microbial community of field crickets – Soon Hwee Ng – Ecology and Evolution

Comparison of closely related, uncultivated Coxiella tick endosymbiont population genomes reveals clues about the mechanisms of symbiosis – Despina Tsementzi – Environmental Microbiology

Insights into the bacterial symbiont diversity in spiders – Lihua Zhang – Ecology and Evolution

Plant, root, and soil microbiome

Legume endosymbionts: Drought stress tolerance in second‐generation chickpea (Cicer arietinum) seeds – V Kumari – Journal of Agronomy and Crop Science

Quantifying the Spatiotemporal Dynamics of Plant Root Colonization by Beneficial Bacteria in a Microfluidic Habitat – Jayde A Aufrecht – Advanced Biosystems

Response of the wheat rhizosphere soil nematode community in wheat/walnut intercropping system in Xinjiang, Northwest China – Peng-hua Bai – Applied Entomology and Zoology

Pre-print: Host identity and functional traits determine the community composition of the arbuscular mycorrhizal fungi in facultative epiphytic plant species – Maria del Mar Alguacil – bioRxiv

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

Water and extremophile microbiome

Impacts of elevated atmospheric CO2 concentration on terrestrial-aquatic carbon transfer and a downstream aquatic microbial community – Emma Rochelle-Newell – Aquatic Sciences

Community differentiation of bacterioplankton in the epipelagic layer in the South China Sea – Yi Zhang – Ecology and Evolution

Built environment

Review: Ecotoxicological effects of microplastics on biota: a review – Sadasivam Anbumani – Environmental Science and Pollution Research

Bioinformatics

Renewing Felsenstein’s phylogenetic bootstrap in the era of big data – F Lemoine – Nature

Pre-print: Machine learning based prediction of functional capabilities in metagenomically assembled microbial genomes – Fred Farrell – bioRxiv

Techniques

Review: Overview of Next‐Generation Sequencing Technologies – Barton E Slatko – Current Protocols in Molecular Biology

More microbes

Deep mitochondrial origin outside the sampled alphaproteobacteria – Joran Martijn – Nature

Evolutionary novelty in gravity sensing through horizontal gene transfer and high-order protein assembly – Tu Ahn Nguyen – PLOS Biology

Pre-print: Differentiation of vegetative cells into spores: a kinetic model applied to Bacillus subtilis – Emilie Gauvry – bioRxiv

Pre-print: A decay effect of bacterial growth rate associated with genome reduction – Kouhei Tsuchiya – bioRxiv

Microbes in the news

Mass suicide documented in bacteria – Nature

Researchers assassinate disease-causing bacteria with virus cocktail – EurekAlert

Bacteria in the small intestine indispensable for fat absorption – EurekAlert

Why a rinse won’t do: on menstrual cups, bacteria, and toxic shock syndrome – Siouxsie Wiles – The Spinoff

Study reveals how bacteria communicate in groups to avoid antibiotics – EurekAlert

Podcast: Gut Punch – Marketing Microbiome Hype – Michael Joyce – Health News Review

Microbes on the market

Global Microbiome Therapeutics Market to Witness Comprehensive Growth By 2024 – Healthcare Trends

uBiome Sponsors Annual Fundraising Walk, SF Take Steps, to Support the Crohn’s and Colitis Foundation – benzinga

Microbiome Company A-Mansia Secures €16M – Allison Johnson – Biocentury

Science, career, and publishing

A photo celebration of scientists at work – Jack Leeming – Nature

Scientists’ early grant success fuels further funding – Holly Else – Nature

Pre-print: Strength in numbers: collaborative science for new experimental model systems – Ross F Waller – 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 24, 2018

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Today, after a hiatus, we have a new and big digest. Have a good Tuesday!

Gut Or General Microbiome

Editorial: Metagenomics, culturomics, and the human gut microbiota – Sophie Amrane – Expert Review of Anti-infective Therapy

Review: Disruptions in gut microbial-host co-metabolism and the development of metabolic disorders – Cynthia Rajani – Clinical Science

Metabolic retroconversion of trimethylamine N-oxide and the gut microbiota – Lesley Hoyles – Microbiome

Review: Factors influencing horizontal gene transfer in the intestine – Ximin Zeng – Animal Health Research Reviews

Commentary: Help, hope and hype: ethical considerations of human microbiome research and applications – Yonghui Ma – Protein & Cell

A System Biology Perspective on Environment-Host-Microbe Interactions – Lianmin Chen – Human Molecular Genetics

Comment on: effects of sleeve gastrectomy on the composition and diurnal oscillation of gut microbiota related to the metabolic improvements – Tammy L.Kindel – Surgery for Obesity and Related Diseases

Dietary Interventions to Modulate the Gut Microbiome—How Far Away Are We From Precision Medicine – Francesca De Filippis – Inflammatory Bowel Diseases

Targeting the gut microbiome to treat the osteoarthritis of obesity – Eric M. Schott – JCI Insight

Increased prevalence of pathogenic bacteria in the gut microbiota of infants at risk of developing celiac disease: the PROFICEL study – Marta Olivares –  Gut Microbes

Genome sequence and description of Gracilibacillus timonensis sp. nov. strain Marseille-P2481T , a moderate halophilic bacterium isolated from the human gut microflora – Awa Diop – Microbiology Open

Inflammasomes make the case for littermate-controlled experimental design in studying host-microbiota interactions – Michail Mamantopoulos – Gut Microbes

No Significant Association Between the Fecal Microbiome and the Presence of Irritable Bowel Syndrome-type Symptoms in Patients with Quiescent Inflammatory Bowel Disease – Oliver Shutkever –  Inflammatory Bowel Diseases

Research Highlight: Microbiome promotes pancreatic cancer – Iain Dickson – Nature Reviews Gastroenterology & Hepatology

Deciphering human gut microbiota-nutrient interactions: a role for biochemistry – Carina Chittim – Biochemistry

Letter: Defining the Impact of Host Genotypes on Microbiota Composition Requires Meticulous Control of Experimental Variables –  Andy Wullaert – Cell Immunity

Review: Engineered Human Gastrointestinal Cultures to Study the Microbiome and Infectious Diseases – Sarah E.Blutt – Cellular and Molecular Gastroenterology and Hepatology

The Role of Macrophage Migration Inhibitory Factor in the Function of Intestinal Barrier – Milica Vujicic- Scientific Reports

Perspective: Urbanization and the gut microbiota in health and inflammatory bowel disease – Tao Zuo – Nature Reviews Gastroenterology & Hepatology

A systems biology approach to predict and characterize human gut microbial metabolites in colorectal cancer – QuanQiu Wang – Scientific Reports

Review: The human gut microbiota: metabolism and perspective in obesity – Aline Corado Gomes – Gut Microbes

Association between the Dietary Inflammatory Index (DII) and urinary enterolignans and C-reactive protein from the National Health and Nutrition Examination Survey-2003-2008 – Nitin Shivappa – European Journal of Nutrition

Case Report: The Effect of Fecal Microbiota Transplantation on a Child with Tourette Syndrome – Huijun Zhao – Case Reports in Medicine

Current evidence linking diet to gut microbiota and brain development and function – Florencia Ceppa – International Journal of Food Sciences and Nutrition

Using standard microbiome reference groups to simplify beta-diversity analyses and facilitate independent validation – Marlena Maziarz – Bioinformatics

Review: Gut microbiota, metabolism and psychopathology: A critical review and novel perspectives – Robin N. Groen – Critical Reviews in Clinical Laboratory Sciences

The Role of Gut Microbiota in Obesity and Type 2 and Type 1 Diabetes Mellitus: New Insights into “Old” Diseases – Igor Alexander Harsch – Medical Sciences

Biogeography and environmental conditions shape bacteriophage-bacteria networks across the human microbiome – Geoffrey D. Hannigan – PLoS Computational Biology

 

Respiratory Microbiome

Prenatal antibiotic exposure and childhood asthma: a population-based study – Keely Loewen – European Respiratory Journal

Impact of gut colonization with butyrate producing microbiota on respiratory viral infection following allo-HCT – Bastiaan W. Haak – Blood

Oropharyngeal and nasopharyngeal decontamination with chlorhexidine gluconate in lung cancer surgery: a randomized clinical trial – Xavier Benoit D’Journo – Intensive Care Medicine

Impact of Long-Term Erythromycin Therapy on the Oropharyngeal Microbiome and Resistance Gene Reservoir in Non-Cystic Fibrosis Bronchiectasis – Jocelyn M. Choo – mSphere

Neonates colonized with pathogenic bacteria in the airways have a low-grade systemic inflammation – Nadia Rahman Fink – Allergy

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

 

Oral Microbiome

Metagenomic analysis of oral microbiome in young children aged 6‐8 y living in a rural isolated Chinese province – Yuan Xu – Oral Diseases

Microbiota and Metatranscriptome Changes Accompanying the Onset of Gingivitis – Emily M. Nowicki – mBio

Do we treat our patients or rather periodontal microbes with adjunctive antibiotics in periodontal therapy? A 16S rDNA microbial community analysis – Daniel Hagenfeld – PLoS One

The interplay between oral microbiome, lifestyle factors and genetic polymorphisms in the risk of oral squamous cell carcinoma – Jenn-Ren Hsiao – Carcinogenesis

Dynamic Alterations in Salivary Microbiota Related to Dental Caries and Age in Preschool Children With Deciduous Dentition: A 2-Year Follow-Up Study – Lei Xu – Frontiers in Physiology

 

Reproductive / Urinary tract Microbiome

How uterine microbiota might be responsible for a receptive, fertile endometrium – Marilen Benner – Human Reproduction Update

Culturing of female bladder bacteria reveals an interconnected urogenital microbiota – Krystal Thomas-White – Nature Communications

 

Fecal Microbiota Transplant

Editorial: Is fecal microbiota transplantation a temporary patch for treatment of Clostridium difficile infection or a new frontier of therapeutics? – Alexander Khoruts – Expert Review of Gastroenterology & Hepatology

Case Report: ANCA Vasculitis and Hemophagocytic Lymphohistiocytosis following a Fecal Microbiota Transplant – Adam Amlani – Case Reports in Rheumatology

Regional variability in fecal microbiota transplantation practices: a survey of the Southern Ontario Fecal Microbiota Transplantation Movement – Susy S. Hota – CMAJ Open

Commentary: Bacteriophage transfer during faecal microbiota transplantation in Clostridium difficile infection is associated with treatment outcome – Blessing O. Anonye – Frontiers in Cellular and Infection Microbiology

Fecal microbiota transplantation reverses antibiotic and chemotherapy-induced gut dysbiosis in mice – Quentin Le Bastard – Scientific Reports

 

Animal Microbiome and Animal Experiments

Evaluation of a therapy for Idiopathic Chronic Enterocolitis in rhesus macaques (Macaca mulatta) and linked microbial community correlates – Joshua M. Taylor​​ – PeerJ

Comparative analyses of the gut microbiota among three different wild geese species in the genus Anser – Wen Wang – Journal of Basic Microbiology

Exposure to concentrated ambient PM2.5 alters the composition of gut microbiota in a murine model – Wanjun Wang – Particle and Fibre Toxicology

Imidacloprid decreases honey bee survival but does not affect the gut microbiome – Kasie Raymann – Applied and Environmental Microbiology

Letter: Bile Acids and the Microbiome in the Cow: Lack of Deoxycholic Acid Hydroxylation – Alan F. Hofmann – Lipids

Akkermansia muciniphila can reduce the damage of gluco/lipotoxicity, oxidative stress, and inflammation and normalize intestine microbiota in streptozotocin-induced diabetic rats – Ling Zhang – Pathogens and Disease

The impact of genome variation and diet on the metabolic phenotype and microbiome composition of Drosophila melanogaster – Lisa Jehrke –  Scientific Reports

Fecal microbial composition associated with variation in feed efficiency in pigs depends on diet and sex – Lisanne M G Verschuren – Journal of Animal Science

Discovery of a mcr-1-bearing plasmid in commensal colistin-resistant Escherichia coli from healthy broilers in Faisalabad, Pakistan – Jiali Lv – Virulence

Pre-colonization with the commensal fungus Candida albicans reduces murine susceptibility to Clostridium difficile infection – Laura Markey – Gut Microbes

PCBs-high-fat diet interactions as mediators of gut microbiota dysbiosis and abdominal fat accumulation in female mice – Yulang Chi – Environmental Pollution

Metagenome and Culture-Based Methods Reveal Candidate Bacterial Mutualists in the Southern House Mosquito (Diptera: Culicidae) – Aparna Telang – Journal of Medical Entomology

Polysaccharide of Hericium erinaceus attenuates colitis in C57BL/6 mice via regulation of oxidative stress, inflammation-related signaling pathways and modulating the composition of the gut microbiota – Yilin Ren – The Journal of Nutritional Biochemistry

Potent SGLT1/2 Dual Inhibition Improves Glycemic Control Without Marked Gastrointestinal Adaptation or Colonic Microbiota Changes in Rodents – Fuyong Du – Journal of Pharmacology and Experimental Therapeutics

Similarity of the dog and human gut microbiomes in gene content and response to diet – Luis Pedro Coelho – Microbiome

Direct and Indirect Effects of Penguin Feces on Microbiomes in Antarctic Ornithogenic Soils – Yudong Guo – Frontiers in Microbiology

Stem Cell Transcription Factor FoxO Controls Microbiome Resilience in Hydra – Benedikt M. Mortzfeld – Frontiers in Microbiology

The effects of baicalein on cortical pro-inflammatory cytokines and the intestinal microbiome in senescence accelerated mouse prone 8 – Li Gao – ACS Chemical Neuroscience

Biases from different DNA extraction methods in intestine microbiome research based on 16S rDNA sequencing: a case in the koi carp, Cyprinus carpio var. Koi – Zhuoran Han – Microbiology Open

 

Built Environments

A comparison of methods used to unveil the genetic and metabolic pool in the built environment – Cinta Gomez-Silvan – Microbiome

Metabolism and Biodegradation of Spacecraft Cleaning Reagents by Strains of Spacecraft-Associated Acinetobacter – Mogul Rakesh – Astrobiology

 

Pathogen Research

The Critical Role of Zinc in a New Murine Model of Enterotoxigenic  E. coli 1 (ETEC) Diarrhea – DT Bolick  – Infection and Immunity

Review: Effects of antibiotic resistance (AR) and microbiota shifts on Campylobacter jejuni-mediated diseases – Phillip T. Brooks – Animal Health Research Reviews

A quality improvement initiative to reduce necrotizing enterocolitis across hospital systems – Amy T. Nathan – Journal of Perinatology

Quantitative Simulations Predict Treatment Strategies Against Fungal Infections in Virtual Neutropenic Patients – Sandra Timme – Frontiers in Immunology

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

Heterogeneous ceramide distributions alter spatially resolved growth of Staphylococcus aureus on human stratum corneum – Joseph M. Cleary – Journal of the Royal Society Interface

 

Viruses

Viral Diversity of House Mice in New York City – Simon H. Williams – mBio

Subclinical cytomegalovirus infection associates with altered host immunity, gut microbiota and vaccine responses – Clarissa Santos Rocha – Journal of Virology

 

Antimicrobial Research

Antimicrobial resistance: from basic science to translational innovation – Jun Lin –  Animal Health Research Reviews

 

Plant/Environment Microbiome

Drought delays development of the sorghum root microbiome and enriches for monoderm bacteria – Ling Xu – PNAS

Assessment of toxic impact of metals on proline, antioxidant enzymes, and biological characteristics of Pseudomonas aeruginosa inoculated Cicer arietinum grown in chromium and nickel-stressed sandy clay loam soils – Saima Saif – Environmental Monitoring and Assessment

The first Taxus rhizosphere microbiome revealed by shotgun metagenomic sequencing – Da‐Cheng Hao – Journal of Basic Microbiology

Exposure to nanoplastics disturbs the gut microbiome in the soil oligochaete Enchytraeus crypticus – Bo-Kai Zhu – Environmental Pollution

Comparative Microbiome Analysis of a Fusarium Wilt Suppressive Soil and a Fusarium Wilt Conducive Soil From the Châteaurenard Region – Katarzyna Siegel-Hertz – Frontiers in Microbiology

 

Food Microbes

Towards better microbial safety of fresh produce: Chlorophyllin-based photosensitization for microbial control of foodborne pathogens on cherry tomatoes – Egle Paskeviciute – Journal of Photochemistry and Photobiology B: Biology

Metaproteomics of Microbiota in Naturally Fermented Soybean Paste, Da‐jiang – Ping Zhang – Journal of Food Science

 

Drugs, Beneficial Microbes and Compounds

Age-Related Changes in the Natural Killer Cell Response to Seasonal Influenza Vaccination Are Not Influenced by a Synbiotic: a Randomised Controlled Trial – Agnieszka Przemska-Kosicka – Frontiers in Immunology

4G-β-D-galactosylsucrose as a prebiotics may improve underweight in inpatients with schizophrenia – Takahiko Nagamine – Nihon Shokuhin Men’eki Gakkai

An approach on the potential use of probiotics in the treatment of skin conditions: acne and atopic dermatitis – Vitória H. M. Mottin – International Journal of Dermatology

Effects of Prebiotic Fiber Xylooligosaccharide in Adenine induced Nephropathy in Mice – Jieping Yang – Molecular Nutrition and Food Research

Anti-inflammatory effect of multistrain probiotic formulation (L. rhamnosus, B. lactis, and B. longum) – Marzia Sichetti – Nutrition

A combination of Lactobacillus mali APS1 and dieting improved the efficacy of obesity treatment via manipulating gut microbiome in mice – Yung-Tsung Chen – Scientific Reports

The Potential Effect of Chinese Herbal Formula Hongqijiangzhi Fang in Improving NAFLD: Focusing on NLRP3 Inflammasome and Gut Microbiota – Shu Liang – Evidence-Based Complementary and Alternative Medicine

Cationic amphiphilic bolaamphiphile-based delivery of antisense oligonucleotides provides a potentially microbiome sparing treatment for C. difficile – Arun K. Sharma – The Journal of Antibiotics

A probiotic modulates the microbiome and immunity in multiple sclerosis – Stephanie K. Tankou – Annals of Neurology

Comprehensive comparison of polysaccharides from Ganoderma lucidum and G. sinense: chemical, antitumor, immunomodulating and gut-microbiota modulatory properties – Li-Feng Li – Scientific Reports

Anti-diabetic mechanism of dietary polysaccharides based on their gastrointestinal functions – Jie-Lun Hu – Journal of Agricultural and Food Chemistry

The Effects of Synbiotic Supplementation on Body Mass Index, Metabolic and Inflammatory Biomarkers, and Appetite in Patients with Metabolic Syndrome: A Triple-Blind Randomized Controlled Trial – Samira Rabiei – Journal of Dietary Supplements

 

Bioinformatics and Methods

MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs – Daniel H. Huson – Biology Direct

KDiamend: a package for detecting key drivers in a molecular ecological network of disease – Mengxuan Lyu – BMC Systems Biology

ViDiT-CACTUS: an inexpensive and versatile library preparation and sequence analysis method for virus discovery and other microbiology applications – Joost Theo Petra Verhoeven – Canadian Journal of Microbiology

Phylogenomic Analysis of β-Lactamase in Archaea and Bacteria Enables the Identification of Putative New Members – Vivek Keshri – Genome Biology and Evolution

 

16 April, 2018

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Today’s digest is packed with exciting research on links between gut microbiome and bone generation/development, also an interesting approach to fecal metabolome sampling

Gut Microbiome

Gut Microbiome and Bone.Ibáñez L. Joint Bone Spine

The protective effect of Lactobacillus and Bifidobacterium as the gut microbiota members against chronic urticaria.Rezazadeh A. International Immonopharmacology

Exposure to the gut microbiota drives distinct methylome and transcriptome changes in intestinal epithelial cells during postnatal development.Pan WH. Genome Medicine

Fecal Microbiome

Restoration of short chain fatty acid and bile acid metabolism following fecal microbiota transplantation in patients with recurrent Clostridium difficile infection.Seekatz AM. Anaerobe

Clostridium difficile stool shedding in infants hospitalized in two neonatal intensive care units is lower than previous point prevalence estimates using molecular diagnostic methods.Hines AG. BMC Pediatrics

 

Plant, Soil, and Water Microbiome

Metataxonomy and functionality of wood-tar degrading microbial consortia.Brusetti L. Journal of Hazardous Materials

In situ microbiota distinguished primary anthropogenic stressor in freshwater sediments.Xie Y. Environmental Pollution

Biogas production and microbial community properties during anaerobic digestion of corn stover at different temperatures.Liu C. Bioresource Technology

Cadmium exposure and <i>Sedum alfredii</i> planting interactions shape the bacterial community in rhizosphere of the hyperaccumulator plant. Hou D. Applied Environmental Microbiology

Animal Experiments and Microbiome

The effect of resistant starch (RS) on the bovine rumen microflora and isolation of RS-degrading bacteria. Jung DH. Applied Microbiology and Biotechnology

Comparative biogeography of the gut microbiome between Jinhua and Landrace pigs.Xiao Y. Scientific Reports

Changes in the Rumen Epithelial Microbiota and Host Gene Expression of Cattle in Response to Alterations in Dietary Carbohydrate Composition.Petri RM. Applied Environmental Microbiology

Preprint

Mercury methylating microbial communities of boreal forest soils

Jingying Xu. bioRxiv

Techniques

Rat Fecal Metabolomics-Based Analysis.Deda O. Methods in Molecular Biology: Metabolic Profiling

Correction

Correction: <i>’Microbes in sport’ -The potential role of the gut microbiota in athlete health and performance</i>.British Journal of Sports Medicine

April 10, 2018

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After a brief hiatus, your Digest is back! After screening several hundred papers, progress seems to concentrate on a selected fields, including human gut microbiome and plant/soil microbiome. The WHO advocates for a global atlas of zoonotic viruses, a PDF link to a book volume full of application of microbiome engineering in agriculture, environmental protection and industry, and 16s rDNA primers can cross-react with mitochondrial sequences in eukaryotic cells. Last but not least, what can we all do to help young scientists, including ourselves, cope with immense pressure and distress?

General microbiology

Role of Partially Saturated Canthaxanthin and Ergosterol in the Survival of Aspergillus carbonarius Mutant at Extreme Acidic Condition – A. Kumar et al. – Microbiology

Coupled iron-microbial catalysis for CO2 hydrogenation with multispecies microbial communities – Elise Blanchet et al. – Chemical Engineering Journal

An integrated membrane bioreactor system with iron-dosing and side-stream co-fermentation for enhanced nutrient removal and recovery: System performance and microbial community analysis – Ruo-hong Li et al. – Bioresource Technology

The Microbiome and Population Health: Considerations to Enhance Study Design and Data Analysis in Observational and Interventional Epidemiology – Ryan T Demmer – American Journal of Epidemiology

Robust, linear correlations between growth rates and β-lactam–mediated lysis rates – Anna J. Lee et al. – PNAS USA

Human oral microbiome

Apical periodontitis: preliminary assessment of microbiota by 16S rRNA high throughput amplicon target sequencing – Federico Mussano and Ilario Ferrocino et al. – BMC Oral Health

Human gut microbiome

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

Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction – Xin Zhou, Jing Li and Junli Guo et al. – Microbiome

Book chapter: Influence of the Gut Microbiome on Immune Development During Early Life – Shankar S. Iyer and Richard S. Blumberg – Physiology of the Gastrointestinal Tract (Sixth Edition)

Book chapter: Gut Barrier: Innate Immunity – Gerco den Hartog et al. – Physiology of the Gastrointestinal Tract (Sixth Edition)

Review: Molecular Pathophysiology of Epithelial Barrier Dysfunction in Inflammatory Bowel Diseases – Jessica Y. Lee et al. – Proteomes

Impact of tart cherries polyphenols on the human gut microbiota and phenolic metabolites in vitro and in vivo – Alba C. Mayta-Apaza et al. – The Journal of Nutritional Biochemistry

Characterization of the duodenal bacterial microbiota in patients with pancreatic head cancer vs. healthy controls – Qi-Xiang Mei et al. – Pancreatology

Human multi-site microbiome

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

Animal experiments

Nile tilapia: Effects of Lactogen 13, a New Probiotic Preparation, on Gut Microbiota and Endocrine Signals Controlling Growth and Appetite of Oreochromis niloticus Juveniles – Gioacchini Giorgia et al. – Microbial Ecology

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

Gut Microbiota Promotes Tumor Growth in Mice by Modulating Immune Response – Vrishketan Sethi et al. – Gastroenterology

The effects of feeding monensin on rumen microbial communities and methanogenesis in bred heifers fed in a drylot – E.A. Melchior et al. – Livestock Science

Identification, characterization and selection of autochthonous lactic acid bacteria as probiotic for feedlot cattle – Natalia C. Maldonado et al. – Livestock Science

Glyphosate based- herbicide exposure affects gut microbiota, anxiety and depression-like behaviors in mice – Yassine Aitbali et al. – Neurotoxicology and Teratology

Animal microbiome

Characterization of the bacterial community in different parts of the gut of sea cucumber (Apostichopus Japonicus) and its variation during gut regeneration – Luo Wang et al. – Aquaculture Research

Review: The adherence and colonization of microorganisms in fish gastrointestinal tract – Xuemei Li et al. – Reviews in Aquaculture

Effect of Saccharomyces boulardii and Bacillus subtilis B10 on gut microbiota modulation in broiler – Chubin Qin and Li Gong et al. – Animal Nutrition

Metabolomics Study of Immune Responses of New Zealand Greenshell™ Mussels (Perna canaliculus) Infected with Pathogenic Vibrio sp. – Thao V. Nguyen et al. – Marine Biotechnology

Review: Use of antibiotics in broiler production: Global impacts and alternatives – Youcef Mehdi et al. – Animal Nutrition

Food Microbiome

PDF: High-Throughput rRNA Gene Sequencing Reveals High and Complex Bacterial Diversity Associated with Brazilian Coffee Bean Fermentation – Dão Pedro de Carvalho Neto et al. – Food Technology and Biotechnology

The impact of vegan production on the kimchi microbiome – Michelle Zabat et al. – Food Microbiology

Plant, root and soil microbiome

Soil abiotic variables are more important than Salicaceae phylogeny or habitat specialization in determining soil microbial community structure – Sonya Erlandson et al. – Molecular Ecology

RNA-based analyses reveal fungal communities structured by a senescence gradient in the moss Dicranum scoparium and the presence of putative multi-trophic fungi – Ko‐Hsuan Chen et al. – New Phytologist

Microbial diversity changes with rhizosphere and hydrocarbons in contrasting soils – Muhammad Atikul Islam Khan et al. – Ecotoxicology and Environmental Safety

Effects of redox potential on soil Cadmium solubility: Insight into microbial community – Delong Meng et al. – Journal of Environmental Sciences

Long-term phosphorus application to a maize monoculture influences the soil microbial community and its feedback effects on maize seedling biomass – Ming Lang et al. – Applied Soil Ecology

Book chapter: Differential Responses of Plants to Biotic Stress and the Role of Metabolites – Maham Saddique et al. – Plant Metabolites and Regulation Under Environmental Stress

Role of Phenolic Acids from the Rhizosphere Soils of Panax notoginseng as a Double-Edge Sword in the Occurrence of Root-Rot Disease – Ya-Meng Zhao et al. – Molecules

Forum: From Petri Dishes to Model Ecosystems – Oskar Siemianowski et al. – Trends in Plant Science

An Insight into Catechins Metabolic Pathways of Camellia sinensis Based on Genome and Transcriptome Analysis – Wenzhao Wang et al. – Journal of Agricultural and Food Chemistry

Seasonal characterization of sugarcane vinasse: Assessing environmental impacts from fertirrigation and the bioenergy recovery potential through biodigestion – Lucas Tadeu Fuess et al. – Science of The Total Environment

Soil microbial biomass: A key soil driver in management of ecosystem functioning – Jay Shankar Singh and Vijay Kumar Gupta – Science of The Total Environment

Phosphorus fertilising potential of fly ash and effects on soil microbiota and crop – Deborah Schönegger et al. – Resources, Conservation and Recycling

Response of the soil microbial community to different fertilizer inputs in a wheat-maize rotation on a calcareous soil – Shuikuan Bei et al. – Agriculture, Ecosystems & Environment

Water and extremophile microbiome

Bacterial Diversity and Functional Activity of Microbial Communities in Hot Springs of the Baikal Rift Zone – E. V. Lavrentyeva et al. – Microbiology

Microbial Community Composition and Rates of the Methane Cycle Microbial Processes in the Upper Sediments of the Yamal Sector of the Southwestern Kara Sea – A. S. Savvichev et al. – Microbiology

Nematode-associated microbial taxa do not correlate with host phylogeny, geographic region or feeding morphology in marine sediment habitats – Taruna Schuelke et al. – Molecular Ecology

Discriminating activated sludge flocs from biofilm microbial communities in a novel pilot-scale reciprocation MBR using high-throughput 16S rRNA gene sequencing – Ryan De Sotto et al. – Journal of Environmental Management

PDF: Divergent assemblage patterns of abundant and rare microbial sub-communities in response to inorganic carbon stresses in a simultaneous anammox and denitrification (SAD) system – Duntao Shu et al. – Bioresource Technology

Antibiotic resistance in wastewater treatment plants: Tackling the black box – Célia M. Manaia et al. – Environment International

Phages and viruses

** Building a global atlas of zoonotic viruses – Dennis Carroll et al. – Bulletin of WHO

Phages infecting Faecalibacterium prausnitzii belong to novel viral genera that help to decipher intestinal viromes – Jeffrey K. Cornuault et al. – Microbiome

Dual Insect specific virus infection limits Arbovirus replication in Aedes mosquito cells – Michaela J. Schultz et al. – Virology

Technology

** Taxon Disappearance from Microbiome Analysis Reinforces the Value of Mock Communities as a Standard in Every Sequencing Run – Yi-Chun Yeh et al. – mSystems

Hemolymph Microbiomes of Three Aquatic Invertebrates as Revealed by a New Cell Extraction Method – Xinxu Zhang et al. – Applied and Environmental Microbiology

Clinical impact of rapid bacterial identification by MALDI-TOF MS combined with the bêta-LACTA™ test on early antibiotic adaptation by an antimicrobial stewardship team in bloodstream infections – A. Mizrahi et al. – Infectious Diseases

Genetic engineering of bee gut microbiome bacteria with a toolkit for modular assembly of broad-host-range plasmids – Sean P. Leonard et al. – ACS Synthetic Biology

** Cross-Reactivity of Prokaryotic 16S rDNA-Specific Primers to Eukaryotic DNA: Mistaken Microbial Community Profiling in Environmental Samples – Shailendra Yadav et al. – Current Microbiology

Detection of Pathogenic Microorganisms by Microfluidics Based Analytical Methods – Dongxue Zhang et al. – Analytical Chemistry

** Book chapter PDF: Microbial, Plant, Environmental and Industrial Technologies – Debmalya Barh and Vasco Azevedo – Microbial Omics: Applications in Biotechnology

Metabolome- and genome-scale model analyses for engineering of Aureobasidium pullulans to enhance polymalic acid and malic acid production from sugarcane molasses – Jun Feng and Jing Yang et al. – Biotechnology for Biofuels

eDNA-based bioassessment of coastal sediments impacted by an oil spill – Yuwei Xie et al. – Environmental Pollution

Using natural biomass microorganisms for drinking water denitrification – Darleila Damasceno Costa et al. – Journal of Environmental Management

Bioinformatics

Cluster and Multiple Correspondence Analyses in Rheumatology: Paths to Uncovering Relationships in a Sea of Data – Lu Han et al. – Rheumatic Disease Clinics of North America

Microbes in the news

Faecal transplantation: do not try this at home – Talha Khan Burki – The Lancet Gastroenterology & Hepatology

Non-microbiology picks

** Editorial: Time to talk about why so many postgrads have poor mental health – Nature

Editorial: Using Preprints for Journal Clubs – Arturo Casadevall and Neil Gow – mBio

 

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