February 3, 2018

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Today’s digest is short, but has exciting reads on how machine learning is improving prediction of antibiotic resistance genes.

General Microbiome

Construction of Effective Minimal Active Microbial Consortia for Lignocellulose Degradation. Puentes-Téllez PE. Microbial Ecology

Review: Role of antimicrobial peptides in controlling symbiotic bacterial populations. Mergaert P. Natural Product Reports

Evaluation of the ability of commercial wine yeasts to form biofilms (mats) and adhere to plastic: implications for the microbiota of the winery environment.Tek EL. FEMS Microbiology Ecology

Gut Microbiome

The mechanistic link between health and gut microbiota diversity.Larsen OFA. Scientific Reports

REVIEW:The Role of Gut Microbiome and Associated Metabolome in the Regulation of Neuroinflammation in Multiple Sclerosis and Its Implications in Attenuating Chronic Inflammation in Other Inflammatory and Autoimmune Disorders.Dopkins N. Immunology

Plant, Soil, and Water Microbiome

Lithobiontic life: “Atacama rocks are well and alive”. Gómez-Silva B.Antonie Van Leeuwenhoek

Contrasting patterns of the bacterial and archaeal communities in a high-elevation river in northwestern China. Hu Y. Journal of Microbiology

Arbuscular Mycorrhizal Fungi and Plant Chemical Defence: Effects of Colonisation on Aboveground and Belowground Metabolomes. Hill EM. Journal of Chemical Ecology

Comparison of plants with C3 and C4 carbon fixation pathways for remediation of polycyclic aromatic hydrocarbon contaminated soils. Sivaram AK. Scientific Reports

Soda pans of the Pannonian steppe harbor unique bacterial communities adapted to multiple extreme conditions. Szabó A. Exremophiles

The effects of glyphosate, glufosinate, paraquat and paraquat-diquat on soil microbial activity and bacterial, archaeal and nematode diversity.Dennis PG. Scientific Reports

Soil commensal rhizobia promote Rhizobium etli nodulation efficiency through CinR-mediated quorum sensing. Miao J. Archives of Microbiology

Distribution of thermophilic endospores in a temperate estuary indicate that dispersal history structures sediment microbial communities.Bell E. Environmental Microbiology

Animal Experiments and Microbiome

Age-associated microbiome shows the giant panda lives on hemicelluloses, not on cellulose. Zhang W. ISME Journal

Increased productivity in poultry birds by sub-lethal dose of antibiotics is arbitrated by selective enrichment of gut microbiota, particularly short-chain fatty acid producers. Banerjee S. Microbiology

Whole metagenome sequencing reveals links between mosquito microbiota and insecticide resistance in malaria vectors. Dada N. Scientific Reports

Virome

The virome of the arbuscular mycorrhizal fungus Gigaspora margarita reveals the first report of DNA fragments corresponding to replicating non-retroviral RNA viruses in Fungi.Turina M. Environmental Microbiology

Techniques/Protocols

DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data.Arango-Argoty G. Microbiome

February 2, 2018

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Today’s digest is full of exciting microbiome papers and brilliant reviews, including an update on the Human Microbiome Project.

 

General Microbiome

Toward an integrative molecular approach to wildlife disease. DeCandia AL. Conservation Biology

Opinions: Genome watch: Keeping tally in the microbiome.Almeida A. Nature Reviews Microbiology

REVIEW: Cancer immunotherapy in 2017: The breakthrough of the microbiota.Kroemer G. Nature Reviews Immunology

BACTERIOPHAGES OF THE URINARY MICROBIOME.Miller-Ensminger T. Journla of Bacteriology

Gut Microbiome

REVIEW: Influence of functional food components on gut health.Wan MLY. Critical Reviews on Food Science and Nutrition

REVIEW:Gut Microbiota and the Neuroendocrine System. Farzi A. Neurotherapeutics.

Gut as an emerging organ for the treatment of diabetes.Haluzik M. Journal of Endocrinology

Human Microbiome Project

Host genetic variation and its microbiome interactions within the Human Microbiome Project.Kolde R. Genome Medicine

 Skin Microbiome

Commensal microbiota modulate gene expression in the skin.Meisel JS. Microbiome

Plant, Soil, and Water Microbiome

Effect of light wavelength on hot spring microbial mat biodiversity.Nishida A. PLos One

Temperature and nutrients as drivers of microbially mediated arsenic oxidation and removal from acid mine drainage. Tardy V. Applied Microbiology and Biotechnology

Microbial Diversity of Hypersaline Sediments from Lake Lucero Playa in White Sands National Monument, New Mexico, USA.Sirisena KA. Microbial Ecology

Influence of Darkness and Aging on Marine and Freshwater Biofilm Microbial Communities Using Microcosm Experiments. Hede N. Microbial Ecology

REVIEW:Rhizobia: from saprophytes to endosymbionts.Poole P. Nature Reviews Microbiology

Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface.Probst AJ, Ladd B. Nature Microbiology

Inorganic carbon addition stimulates snow algae primary productivity.Hamilton TL. ISME Journal

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline. Broberg M.Microbiome

Microbes participated in macrophyte leaf litters decomposition in freshwater habitat. Zhao B. FEMS Microbiology Ecology

Animal Microbiome and Experiments

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times. Lim JS. Asian-Australasian Journal of Animal Science

Effects of dietary fiber levels on cecal microbiota composition in geese.Li Y. Asian-Australasian Journal of Animal Science

Planktonic microbial profiling in water samples from a Brazilian Amazonian reservoir. Cabral BCA. Microbiology Open

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L.Alberoni D. Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2.Yitbarek A. Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish. Legrand TPRA. Frontiers in Microbiology

Antiobitics

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan.Zhu D. Environmental Science and Technology

February 1, 2018

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The publication of a Springer manual entitled Mechanisms underlying host-microbiome interactions in pathopysiology of human diseases contains multiple interesting articles today, including reviews on the gut microbiome and preterm infant gut development, colerectal cancer, and metabolic disease, as well as a useful review of statistical models for mouse and human microbiome data. In addition, a revisitation of gut enterotypes via metabolomics, decreased Akkermansia muciniphila in psoriasis,  the bacterial communities of fiddler crabs, the impact of different wavelengths of light on hot spring bacteria, and two articles on the uses of metabarcoding in both 16S and eukaryotic microbiota analysis.

Events and jobs

Microbiology Manager – Covance – Indianapolis, Indiana

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Pregnancy and early life

*Review: Impact of Microbes on the Intestinal Development of the Preterm Infant – Elizabeth Humphrey – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Multi-site human microbiome

Review: Good and Bad Farming: The Right Microbiome Protects from Allergy – Markus Johannes Ege – Allergy Prevention and Exacerbation

Human gut microbiome

*Functional metagenomics identifies novel genes ABCTPP, TMSRP1 and TLSRP1 among human gut enterotypes – Manoj Kumar Verma – Scientific Reports

Gastric bacterial Flora in patients Harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – BMC Gasteroentrology

*The Akkermansia muciniphila is a gut microbiota signature in psoriasis – LiRong Tan – Experimental Dermatology

Review: The regulation of host cellular and gut microbial metabolism in the development and prevention of colorectal cancer – Cheng-Bei Zhou – Critical Reviews in Microbiology

Editorial: Unveiling the gut virome in human health and diseases – Tao Zuo – International Journal of Clinical Virology

*Review: The Influence of the Microbiota on the Etiology of Colorectal Cancer – Melissa C. Kordahi – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

*Review: Altered Microbiota and Their Metabolism in Host Metabolic Diseases – Beng San Yeoh –  In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Review: The Gut Microbiome and Its Marriage to the Immune System: Can We Change It All? – Eva Untersmayr – Allergy Prevention and Exacerbation

*Review: Fecal Microbiota Transplants: Current Knowledge and Future Directions – Roxana Chis – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

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Animal experiments

Tissue Level Diet and Sex-by-Diet Interactions Reveal Unique Metabolite and Clustering Profiles Using Untargeted Liquid Chromatography-Mass Spectrometry on Adipose, Skeletal Muscle, and Liver Tissue in C57BL6/J Mice – Ann Wells – Journal of Proteome Research

The Changes of Colonic Bacterial Composition and Bacterial Metabolism Induced by an Early Food Introduction in a Neonatal Porcine Model – Chao Shi – Current Microbiology

Animal microbiome

*Multiple colonist pools shape fiddler crab-associated bacterial communities – Catalina Cuellar-Gempeler – The ISME Journal

Transcriptional changes detected in fecal RNA of neonatal dairy calves undergoing a mild diarrhea are associated with inflammatory biomarkers – Fernanda Rosa – PLOSone

Tiny but mighty: The role of the rumen microbes in livestock production
K M Cammack – Journal of Animal Science

Effects of Spray-Dried Porcine Plasma on Fecal Microbiota in Nursery Pigs – Huyen Tran – Journal of Animal Science

Organic acid production from potato starch waste fermentation by rumen microbial communities from Dutch and Thai dairy cows – Susakul Palakawong Na Ayudthaya – Biotechnology for Biofuels

Plant, root, and soil microbiome

The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C. A. Mallon – The ISME Journal

Stress-Tolerant Beneficial Microbes for Sustainable Agricultural Production – Reeta Goel – In: Microorganisms for Green Revolution. Microorganisms for Sustainability, vol 7. Springer

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire – Taylor K. Dunivin – PLOSone

Review: The Chemistry of Plant-Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance – Msizi Mhlongo – Frontiers in Plant Science

Characterization of bacteria isolated from the Saffron (Crocus Sativus L.) rhizosphere – Majid Jami Al-Ahmadi – Journal of Horticultural Research

Review: Rhizoremediation – Plant Microbe Interactions in the Removal of Pollutants – Mehak Oberai – International Journal of Current Microbiology and Applied Sciences (IJCMAS)

Role of microbes in organic carbon decomposition and maintenance of soil ecosystem – Hina Khatoon – International Journal of Chemical Studies

Water and extremophile microbiome

Vibrio cholerae embraces two major evolutionary traits as revealed by targeted gene sequencing – Kazuhisa Okada – Scientific Reports

*Effect of light wavelength on hot spring microbial mat biodiversity – Akifumi Nishida – PLOSone

Microbial Ecology

Estimating taxon-specific population dynamics in diverse microbial communities – Benjamin J. Koch – Ecosphere

Metabolomic analysis of low and high biofilm-forming Helicobacter pylori strains – Eric Hong Jian Wong – Scientific Reports

Resistome

High dietary zinc feeding promotes persistence of multi-resistant E. coli in the swine gut – Lisa Ciesinski – PLOSone

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Probiotics / prebiotics

An Integrative Review on the Effect of Prebiotics, Probiotics, and Synbiotics on Infection After Colorectal Cancer Surgery – Sarah Williams Anderson – Aorn Journal

Phages and Viruses

Metagenomic Analysis of the Jinding Duck Fecal Virome – Lili Zhao – Current Microbiology

Bioinformatics

*Statistical Models and Analysis of Microbiome Data from Mice and Humans – Yinglin Xia – In: Mechanisms Underlying Host-Microbiome Interactions in Pathophysiology of Human Diseases. Physiology in Health and Disease. Springer

Comparative Analysis of Sequence Clustering Methods for Deduplication of Biological Databases – Qingyu Chen – Journal of Data and Information Quality

Techniques

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving – Clinical Metabolomics

*16S rRNA gene metabarcoding and TEM reveals different ecological strategies within the genus Neogloboquadrina (planktonic foraminifer) – Clare Bird – PLOSone

*Metabarcoding analysis of eukaryotic microbiota in the gut of HIV-infected patients – Ibrahim Hamad – PLOSone

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Microbes in the news

The Germ and the Gene: Gut Bacteria Research Takes a Step Forward – Ruairi MacKenzie – Technology Networks

These bacteria produce gold by digesting toxic metals – EurekaAlert

 

 

January 31, 2018

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Today, research in prediabetes microbiome, bacteriophages in urinary microbiota, several reviews and a good number of papers focused in animal microbiome.

 

Human Microbiome

Review: Influence of functional food components on gut health – Murphy L.Y. Wan – Critical Reviews in Food Science and Nutrition

Review: Gut Microbiota and the Neuroendocrine System – Aitak Farzi – Neurotherapeutics

Laxative effect of repeated Daiokanzoto is attributable to decrease in aquaporin-3 expression in the colon – Risako Kon – Journal of Natural Medicines

Aberrant intestinal microbiota in individuals with prediabetes – Kristine H. Allin – Diabetologia

Perspective: The Potential for Topical Probiotic Treatment of Chronic Rhinosinusitis, a Personal Perspective – Anders U. Cervin – Frontiers in cellular and infection microbiology

The third tier in treatment: Attending to the growing connection between gut health and emotional well-being – Joseph Verdino – Health psychology open

Bifidobacteria and lactobacilli in the gut microbiome of children with non-alcoholic fatty liver disease: which strains act as health players? – Valerio Nobili – Archives of medical science

Kynurenic Acid: The Janus-Faced Role of an Immunomodulatory Tryptophan Metabolite and Its Link to Pathological Conditions – Elisa Wirthgen – Frontiers in immunology

Adaptation of commensal proliferating Escherichia coli to the intestinal tract of young children with cystic fibrosis – Susana Matamouros – Proceedings of the National Academy of Sciences of the United States of America

Review: Gut as an emerging organ for the treatment of diabetes – Martin Haluzik – The Journal of endocrinology

Bacteriophages Of The Urinary Microbiome – Taylor Miller-Ensminger – Journal of bacteriology

Commensal microbiota modulate gene expression in the skin – Jacquelyn S. Meisel – Microbiome

Host genetic variation and its microbiome interactions within the Human Microbiome Project – Raivo Kolde – Genome medicine

 

Animal Microbiome

Comparison of Microbial Communities in Swine Manure at Various Temperatures and storage times – Joung-Soo Lim – Asian-Australasian journal of animal sciences

Effects of different dietary ratio of metabolizable glucose and metabolizable protein on growth performance, rumen fermentation, blood biochemical indices and ruminal microbiota of 8 to 10-month-old heifers – Jie Sun – Asian-Australasian journal of animal sciences

Effects of dietary fiber levels on cecal microbiota composition in geese – Yanpin Li – Asian-Australasian journal of animal sciences

Annotation of gut bacterial taxonomic and functional diversity in Spodoptera litura and Spilosoma obliqua – Kiran G. Bapatla – Journal of Basic Microbiology

Variations in diet cause alterations in microbiota and metabolites that follow changes in disease severity in a multiple sclerosis model – J.E. Libbey – Beneficial Microbes

Impact of beneficial bacteria supplementation on the gut microbiota, colony development and productivity of Apis mellifera L. – D. Alberoni – Beneficial Microbes

Gut microbiota modulates type I interferon and antibody-mediated immune responses in chickens infected with influenza virus subtype H9N2 – A. Yitbarek – Beneficial Microbes

Appropriate dose of Lactobacillus buchneri supplement improves intestinal microbiota and prevents diarrhoea in weaning Rex rabbits – Y. Zhou – Beneficial Microbes

The Inner Workings of the Outer Surface: Skin and Gill Microbiota as Indicators of Changing Gut Health in Yellowtail Kingfish – Thibault P. R. A. Legrand – Frontiers in microbiology

 

Plant/Soil Microbiome

Integrated multi-omic analysis of host-microbiota interactions in acute oak decline – Martin Broberg – Microbiome

Antibiotics Disturb the Microbiome and Increase the Incidence of Resistance Genes in the Gut of a Common Soil Collembolan – Dong Zhu – Environmental science & technology

 

Environmental Microbiome

Coordinated gene expression between Trichodesmium and its microbiome over day–night cycles in the North Pacific Subtropical Gyre – Kyle R Frischkorn – The ISME Journal

 

General Microbiome

Cross-regulatory circuit between AHR and microbiota – Jian Ji – Current Drug Metabolism

‘Massilimalia timonensis’ sp. nov., a new bacterium species isolated from human faeces after decontamination with alcohol – P. Afouda – New microbes and new infections

Taxonomy of anaerobic digestion microbiome reveals biases associated with the applied high throughput sequencing strategies – Stefano Campanaro – Scientific Reports

January 30, 2018

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Today, the exposome on acne, eukaryotes in gut microbiota and chronic fatigue, oral and intestinal microbiome comparison in colorectal cancer, several studies in pathogen research, a review about rhizobia and more!

 

Human Microbiome

Short-Term Overfeeding with Dairy Cream Does Not Modify Gut Permeability, the Fecal Microbiota, or Glucose Metabolism in Young Healthy Men – Beate Ott – The Journal of Nutrition

The influence of exposome on acne – Brigitte Dréno – Journal of the European Academy of Dermatology and Venereology

Geographical Distribution and Diversity of Gut Microbial NADH:Ubiquinone Oxidoreductase Sequence Associated with Alzheimer’s Disease – Elena Paley – Journal of Alzheimer’s Disease

Book review: Microbiota in health and disease: from pregnancy to childhood in Beneficial Microbes

Eukaryotes in the gut microbiota in myalgic encephalomyelitis/chronic fatigue syndrome – Alexandra H. Mandarano – PeerJ

Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study – Edda Russo – Frontiers in Microbiology

Review: The Role of Skin and Orogenital Microbiota in Protective Immunity and Chronic Immune-Mediated Inflammatory Disease – Young Joon Park – Frontiers in Immunology

Short-Chain Fatty Acids Differentially Affect Intracellular Lipolysis in a Human White Adipocyte Model – Johan W. E. Jocken – Frontiers in Endocrinology

Year in Review: Cancer immunotherapy in 2017: The breakthrough of the microbiota – Guido Kroemer – Nature Reviews Immunology

 

Animal Microbiome

Sinus Microanatomy and Microbiota in a Rabbit Model of Rhinosinusitis – Do-Yeon Cho – Frontiers in Cellular and Infection Microbiology

EPSP of L. casei BL23 Protected against the Infection Caused by Aeromonas veronii via Enhancement of Immune Response in Zebrafish – Chubin Qin – Frontiers in Microbiology

Mosquito vector-associated microbiota: Metabarcoding bacteria and eukaryotic symbionts across habitat types in Thailand endemic for dengue and other arthropod-borne diseases – Panpim Thongsripong – Ecology and Evolution

Exogenous Fecal Microbiota Transplantation from Local Adult Pigs to Crossbred Newborn Piglets – Luansha Hu – Frontiers in Microbiology

Composition and Functional Specialists of the Gut Microbiota of Frogs Reflect Habitat Differences and Agricultural Activity – Bing-Hong Huang – Frontiers in Microbiology

Hydrogen-water ameliorates radiation-induced gastrointestinal toxicity via MyD88’s effects on the gut microbiota – Hui-wen Xiao – Experimental & Molecular Medicine

Bacillus licheniformis normalize the ileum microbiota of chickens infected with necrotic enteritis – Shuai Xu – Scientific Reports

 

Beneficial Bacteria and Compounds

Review: Potential interactions among phenolic compounds and probiotics for mutual boosting of their health-promoting properties and food functionalities – A review – Evandro Leite de Souza – Critical Reviews in Food Science and Nutrition

Review: Impact of Dietary Fiber Consumption on Insulin Resistance and the Prevention of Type 2 Diabetes – Martin O Weickert – The Journal of Nutrition

Traditional Herbal Medicine-Derived Sulforaphene LFS-01 Reverses Colitis in Mice by Selectively Altering the Gut Microbiota and Promoting Intestinal Gamma-Delta T Cells – Ming Li – Frontiers in Pharmacology

Antimicrobial activity of apple cider vinegar against Escherichia coli, Staphylococcus aureus and Candida albicans; downregulating cytokine and microbial protein expression – Darshna Yagnik – Scientific Reports

 

Food Microbiome

Assertiveness of meat-borne Lactococcus piscium strains and their potential for competitive exclusion of spoilage bacteria in situ and in vitro – Maik Hilgarth – Journal of Applied Microbiology

 

Pathogen Research

Editorial: Do tetracyclines have the potential to reduce the risk of Clostridium difficile infection? – Sahil Khanna – Expert Review of Anti-infective Therapy

Minireview: Immunological roulette: Luck or something more? Considering the connections between host and environment in TB – John E Pearl – Cellular and Molecular Immunology

Review: Applications for Bacteriophage Therapy during Pregnancy and the Perinatal Period – Lucy L. Furfaro – Frontiers in Microbiology

Antibiotic-Induced Pathobiont Dissemination Accelerates Mortality in Severe Experimental Pancreatitis – Fernanda S. Soares – Frontiers in Immunology

Molecular epidemiology and comparative genomics of Campylobacter concisus strains from saliva, faeces and gut mucosal biopsies in inflammatory bowel disease – Karina Frahm Kirk – Scientific Reports

Exploration of the role of the virulence factor ElrA during Enterococcus faecalis cell infection – Natalia Nunez – Scientific Reports

 

Environmental Microbiome

Review: Rhizobia: from saprophytes to endosymbionts – Philip Poole – Nature Reviews Microbiology

Suppression of the activity of arbuscular mycorrhizal fungi by the soil microbiota – Nanna B Svenningsen – The ISME Journal

 

Microbiology – Other

News and Analysis: Genome watch: Keeping tally in the microbiome – Alexandre Almeida – Nature Reviews Microbiology

 

Non-microbiology picks

A meta-analysis of the diagnostic sensitivity and clinical utility of genome sequencing, exome sequencing and chromosomal microarray in children with suspected genetic diseases – Michelle M Clark – BioRxiv

January 29, 2018

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An exciting fellowship in Ireland, along with some interesting techniques in today’s digest!

Events and jobs
APEX (APC Postdoctoral EXcellence) Fellowship – Ireland
Fellowships will be offered in the four thematic APC research areas of ‘Microbes to Molecules’, ‘Diet and Microbes at the Extremes of Life’, ‘Brain-Gut-Microbiota Axis’ and ‘Host-Microbe Dialogue’. Adhering to the MSCA principle of ‘individual-driven mobility’.

Multi-site human microbiome
Review: Rethinking Antimicrobial Prophylaxis in the Transplant Patient in the World of Emerging Resistant Organisms-Where Are We Today? – Lucy E Horton – Current Hematologic Malignancy Reports

Human gut microbiome
Metabolic mechanisms of interaction within a defined gut microbiota – Gregory Leonard Medlock – bioRxiv

Gastric bacterial flora in patients harbouring Helicobacter pylori with or without chronic dyspepsia: analysis with matrix-assisted laser desorption ionization time-of-flight mass spectroscopy – Verima Pereira – Bmc Gastroenterology

Review: Molecular Paths linking Metabolic Diseases, Gut Microbiota Dysbiosis and Enterobacteria Infections – M Serino – Journal of Molecular Biology
(DOI not availabe yet, linked to PubMed)

Animal microbiome
Metagenomic investigation of vestimentiferan tubeworm endosymbionts from Mid-Cayman Rise reveals new insights into metabolism and diversity – Julie Reveillaud – Microbiome

Microbiome structure influences infection by the parasite Crithidia bombi in bumble bees – Blair K Mockler – Applied And Environmental Microbiology

Plant, root, and soil microbiome
The impact of failure: unsuccessful bacterial invasions steer the soil microbial community away from the invader’s niche – C A Mallon – The Isme Journal

Methanogens are major contributors to nitrogen fixation in soils of the Florida Everglades – Hee-Sung Bae – Applied And Environmental Microbiology

Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence – Jia Liu – Microbiome

Water and extremophile microbiome
Bioavailability of mineral-bound iron to a snow algae-bacteria co-culture and implications for albedo-altering snow algae blooms – Z R Harrold – Applied And Environmental Microbiology

Built environment
Structure, variation, and assembly of the deterioration-associated microbiome of stone monuments – Qiang Li – Applied And Environmental Microbiology

Targeting Bacteria and Methanogens to Understand the Role of Residual Slurry as an Inoculant in Stored Liquid Dairy Manure – Jemaneh Habtewold – Applied And Environmental Microbiology

Techniques
Novel method reveals a narrow phylogenetic distribution of bacterial dispersers in environmental communities exposed to low hydration conditions. – U S Krüger – Applied And Environmental Microbiology

Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling. – Garold Fuks – Microbiome

Microbes in the news
What To Do If You Are Worried About Flesh Eating Bacteria – Bruce Y. Lee – Forbes

Be aware: Certain bacteria may increase HIV risk for women – Hindustan Times (see yesterday’s post for the paper in from Lancet Infectious Diseases)

New Astronaut Food Recipe Combines Human Waste and Bacteria – Jonathan Kesh – Outer Places

‘Bug memories’ could help fight looming crisis – Jamie Morton – New Zealand Herald

January 28, 2018

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A preprint on the gut microbiome of few tribal groups in the Himalayan region; association between vaginal microbiota and HIV;   an integrative approach that encompasses  metatranscriptomics & fatty acid profiling to study the rumen microbiome during feeding;   environmental adaptation shapes the gut microbiota of Rhesus macaques;   microbiome of cactus rhizosphere;   news about uBiome; antibiotics;  and many more articles for today’s digest!

General microbiome

Review: Evolving Ecosystems: Inheritance and Selection in the Light of the Microbiome – S Sandoval-Motta – Archives of Medical Research

Multi-site human microbiome

The nasal microbiome mirrors and potentially shapes olfactory function – K Koskinen – Scientific Reports

Alterations of oral microbiota distinguish children with autism spectrum disorders from healthy controls – Y Qiao – Scientific Reports

Human respiratory microbiome

Pseudomonas aeruginosa Biofilms: Host Response and Clinical Implications in Lung Infections – NM Maurice – American Journal of Respiratory Cell and Molecular Biology

Human skin microbiome

Analysis of the skin mycobiome in adult patients with atopic dermatitis – SH Han – Experimental Dermatology

Human vaginal microbiome

Evaluation of the association between the concentrations of key vaginal bacteria and the increased risk of HIV acquisition in African women from five cohorts: a nested case-control study – RS McClelland – The Lancet

Prevalence of vaginal microorganisms among pregnant women according to trimester and association with preterm birth – K-A Son – Obstetrics & Gynecology Science

Human gut microbiome

Preprint: Gut microbiome transition across a lifestyle gradient in Himalaya – AR Jha – bioRxiv

Physical exercise, gut, gut microbiota, and atherosclerotic cardiovascular diseases – J Chen – Lipids in Health and Disease

Therapeutic Opportunities in Intestinal Microbiota–Virus Interactions – V Monedero – Trends in Biotechnology

Almond Consumption and Processing Affects the Composition of the Gastrointestinal Microbiota of Healthy Adult Men and Women: A Randomized Controlled Trial. – HD Holscher – Nutrients

Effects of Ampicillin on the Gut Microbiome of an Adult Male as Determined by 16S rRNA V4 Metagenomics Sequencing and Greengenes Bioinformatics Suite – K Anukam – Journal of Advances in Microbiology

Determinants of Reduced Genetic Capacity for Butyrate Synthesis by the Gut Microbiome in Crohn’s Disease and Ulcerative Colitis – EJ Laserna-Mendieta – Journal of Crohn’s and Colitis

The Role of Bacteria, Probiotics and Diet in Irritable Bowel Syndrome – A Harper – Foods

Animal experiments 

Preprint: Inter- and intra-domain functional redundancy in the rumen microbiome during plant biomass degradation – A Soellinger – bioRxiv

Gut microbiome may contribute to insulin resistance and systemic inflammation in obese rodents: a meta-analysis. – N Jiao – Physiological Genomics

Protective effect of rosmarinic acid and carnosic acid against streptozotocin-induced oxidation, glycation, inflammation and microbiota imbalance in diabetic rats. – J Ou -Food & Function

Glucocorticoids Drive Diurnal Oscillations in T Cell Distribution and Responses by Inducing Interleukin-7 Receptor and CXCR4 – A Shimba – Immunity

Review: Overview and systematic review of studies of microbiome in schizophrenia and bipolar disorder – TT Nguyen – Journal of Psychiatric Research

Animal microbiome 

Characterization of the Gut Microbiota in Six Geographical Populations of Chinese Rhesus Macaques (Macaca mulatta), Implying an Adaptation to High-Altitude Environment – J Zhao – Microbial Ecology

Opinion: Mission Accomplished? We Need a Guide to the ‘Post Release’ World of Wolbachia for Aedes-borne Disease Control – SA Ritchie – Cell

Microbial community assembly in wild populations of the fruit fly Drosophila melanogaster – KL Adair – The ISME Journal

In silico identification, characterization and expression analysis of attacin gene family in response to bacterial and fungal pathogens in Tenebrio molitor – YH Jo – Entomological Research

Plant, root and soil microbiome

Editorial special issue: the soil, the seed, the microbes and the plant – EB Nelson – Plant and Soil

Complete Genome Sequence of Pseudomonas Parafulva PRS09-11288, a Biocontrol Strain Produces the Antibiotic Phenazine-1-carboxylic Acid – Y Zhang – Current Microbiology

The effects of road building on arbuscular mycorrhizal fungal diversity in Huangshan Scenic Area – A Yang – World Journal of Microbiology & Biotechnology

The role of species turnover in structuring bacterial communities in a local scale in the cactus rhizosphere – VN Kavamura – Plant and Soil

p-Coumaric can alter the composition of cucumber rhizosphere microbial communities and induce negative plant-microbial interactions – X Zhou – Biology and Fertility of Soils

Mycobiomes of sympatric Amorphophallus albispathus (Araceae) and Camellia sinensis (Theaceae) – a case study reveals clear tissue preferences and differences in diversity and composition – M Unterseher – Mycological Progress

Identification, synthesis and regulatory function of the N-acylated homoserine lactone signals produced by Pseudomonas chlororaphis HT66 – H Peng – Microbial Cell Factories

Building Bioeconomy in Agriculture: Harnessing Soil Microbes for Sustaining Ecosystem Services – R Rengalakshmi – Towards a Sustainable Bioeconomy: Principles, Challenges and Perspectives

Competitive traits are more important than stress-tolerance traits in a cadmium-contaminated rhizosphere: a role for trait theory in microbial ecology – JL Wood – Frontiers in Microbiology

Draft Genome Sequence of Pantoea ananatis Strain 1.38, a Bacterium Isolated from the Rhizosphere of Oryza sativa var. Puntal That Shows Biotechnological Potential as an Inoculant – E Megías – Genome Announcements

Copper Bioleaching in China: Review and Prospect – S Yin – Minerals

Water microbiome and extremophiles 

Core promoter information content correlates with optimal growth temperature – AA Aptekmann – Scientific Reports

Food microbiology

Genomic and functional characterisation of two Enterococcus strains isolated from Cotija cheese and their potential role in ripening – M Olvera-García – Applied Microbiology and Biotechnology

Phages and viruses

Review: Phage or foe: an insight into the impact of viral predation on microbial communities – L Fernández – The ISME Journal

Techniques

Artificial Gene Amplification in Escherichia coli Reveals Numerous Determinants for Resistance to Metal Toxicity – KJ Hoegler – Journal of Molecular Evolution

Microbes in the news

uBiome, the Leader in Microbial Genomics, Launches SmartGut and SmartJane Microbiome Test Kits in Canada – Daily Telescope

Niki Bezzant: A gutsful of good health – NZ Herald

How Phenylbutazone, Firocoxib Affect Horses’ Gut Microbiota – the Horse

Botulinum-type toxins jump to a new kind of bacteria – Science Daily

‘Forgotten’ antibiotic offers hope against worst superbugs – Digital Journal

Detect The Level Of Bacteria In Food With This Smartphone-Based System – Wonderful Engineering

When bad bugs jump from farm to bedside – Hutch News

January 27, 2018

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A Saturday digest with lots of fun and weird news of microbiome!
Events and jobs

Adjunct Faculty- Biology, Microbiology, Anatomy & Physiology – St. Louis Community College in Missouri – USA

General microbiome

A Case of Recurrent Pasteurella Bacteremia in an Immunocompetent Patient with No Animal Bite. – F Zarlasht – The American Journal of Case Reports

Pregnancy and early life

Lipopolysaccharide-induced maternal inflammation induces direct placental injury without alteration in placental blood flow and induces a secondary fetal intestinal injury that persists into adulthood. – EM Fricke – American Journal of Reproductive Immunology

Association between duration of intravenous antibiotic administration and early-life microbiota development in late-preterm infants – RD Zwittink – European Journal of Clinical Microbiology & Infectious Diseases

Human gut microbiome

Fungal Diversity of Human Gut Microbiota Among Eutrophic, Overweight, and Obese Individuals Based on Aerobic Culture-Dependent Approach – FM Borges – Current Microbiology

Review: Dietary practices and FODMAPs in South Asia: Applicability of the low FODMAP diet to patients with irritable bowel syndrome – SP Hewawasam – Journal of Gastroenterology and Hepatology

Animal experiments 

Preprint: Mono-Association with Lactobacillus plantarum Disrupts Intestinal Homeostasis in adult Drosophila. – D Fast – bioRxiv

Beneficial effects of Rifaximin in post-infectious irritable bowel syndrome mouse model beyond gut microbiota – Y Jin –  Journal of Gastroenterology and Hepatology

Plant, root and soil microbiome

Predator identity more than predator richness structures aquatic microbial assemblages in Sarracenia purpurea leaves. – EJ Canter – Ecology

Purple corn-associated rhizobacteria with potential for plant growth promotion – A Castellano-Hinojosa – Journal of Applied Microbiology

Fungal diversity in oil palm leaves showing symptoms of Fatal Yellowing disease – OY de Assis Costa – PLoS One

Biosynthetic and antimicrobial potential of actinobacteria isolated from bulrush rhizospheres habitat in Zhalong Wetland, China – Y Li – Archives of Microbiology

Effect of Silene vulgaris and Heavy Metal Pollution on Soil Microbial Diversity in Long-Term Contaminated Soil – M Pacwa-Płociniczak – Water, Air and Soil Pollution

Water microbiome and extremophile 

Ecological and biogeographical drivers of freshwater green algae biodiversity: from local communities to large-scale species pools of desmids – H Bestová – Oecologia

Nitrogen Fixation in Thermophilic Chemosynthetic Microbial Communities Depending on Hydrogen, Sulfate, and Carbon Dioxide –  A Nishihara – J-Stage

Food microbiology

Bacterial community in naturally fermented milk products of Arunachal Pradesh and Sikkim of India analysed by high-throughput amplicon sequencing – HNJ Shangpliang – Scientific Reports

Phages and viruses

Preprint: Diversity and evolution of the emerging Pandoraviridae family – M Legendre – bioRxiv

Microbes in the news

Explore the human microbiome in new Delaware natural history museum exhibit – Delaware Public Media

Thoroughness of panel called into question – Delta Optimist

When DNA Went Mobile Some Archaea Jumped Out of the Hot Tub – GEN News

Scientists find 10 new defense systems used by bacteria – Science News

ASTRONAUTS LIVING IN SPACE CAN EAT BACTERIA THAT FEED ON HUMAN WASTE – Newsweek

A Never-Before-Seen Virus Was Just Found in the Sea, and It Kills Bacteria – Inverse Science

Bacteria block transmission of Zika and Dengue viruses – Medical Xpress

First annual thesis competition held at JMU – The Breeze

Microbiome research refines HIV risk for women – EurekAlert

Shimmery bacteria plus a canvas equals art, briefly – Chicago Tribune

BACTERIA THAT HITCH RIDES ON TOOTHBRUSHES, DIAPERS AND OTHER PLASTIC POLLUTION ARE KILLING CORAL REEFS – Newsweek

 

January 26, 2018

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Here’s your daily Digest after a burst of articles. High-intensity swimming can impact immunity and microbial diversity in mice. Intestinal microbiota can alter host epigenetic in mice. A sad story of an eight year old boy killed by flesh eating bacteria…

Jobs and events

The Human Microbiome – Heidelberg, Germany

2018 MICROBIOME CONFERENCES – Taconic

General microbiology

Peptidoglycan compositional analysis of Enterococcus faecalis biofilm by stable isotope labeling by amino acids in bacterial culture – James D. Chang et al. – Biochemistry

Pregnancy and early life

Vaginal dysbiosis increases risk of preterm fetal membrane rupture, neonatal sepsis and is exacerbated by erythromycin – Richard G. Brown et al. – BMC Medicine

Human skin microbiome

* Review: Skin microbiota–host interactions – Y. Erin Chen et al. – Nature

Human vaginal microbiome

Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim and Yoo Jin Park – Journal of Menopausal Medicine

Human oral microbiome

Silver Fluoride as a Treatment for Dental Caries – J.A. Horst – Advances in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu & Z. Ren et al. – Advances in Dental Research

Video protocol: Oral Biofilm Sampling for Microbiome Analysis in Healthy Children – Elisabeth Santigli et al. – JoVE

Human gut microbiome

Review: Clostridium difficile control measures: current and future methods for prevention – Erik R. Dubberke & Carlos Mejia-Chew – Expert Review of Anti-infective Therapy

Review: Colorectal Cancers: An Update on Their Molecular Pathology – Kentaro Inamura – Cancers

Review: Role of microbiota-derived lipopolysaccharide in adipose tissue inflammation, adipocyte size and pyroptosis during obesity – Lars-Georg Hersoug et al. – Nutrition Research Reviews

* Review: Role of priority effects in the early-life assembly of the gut microbiota – Daniel Sprockett et al. – Nature Reviews Gastroenterology & Hepatology

Review: Upper Respiratory Symptoms, Gut Health and Mucosal Immunity in Athletes – Candice Colbey et al. – Sports Medicine

Review: Microbiota in obesity: interactions with enteroendocrine, immune and central nervous systems – R. J. Mulders et al. – Obesity Reviews

Factors Associated with the Use of Fecal Microbiota Transplant in Patients with Recurrent Clostridium difficile Infections – Sehrish Jamot et al. – Infection Control & Hospital Epidemiology

Animal experiments

Zebrafish: Dysregulation of Intestinal Health by Environmental Pollutants: Involvement of the Estrogen Receptor and Aryl Hydrocarbon Receptor – Lianguo Chen et al. – Environmental Science & Technology

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice – Feifei Lin et al. – Food & Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista et al. – British Journal of Nutrition

Rat: Berberine Modulates Gut Microbiota and Reduces Insulin Resistance via the TLR4 Signaling Pathway – Dan Liu & Yiyi Zhang et al. – Experimental and Clinical Endocrinology & Diabetes

Early microbial colonization affects DNA methylation of genes related to intestinal immunity and metabolism in preterm pigs – Xiaoyu Pan et al. – DNA Research

Mouse: Innate and adaptive lymphocytes sequentially shape the gut microbiota and lipid metabolism – Kairui Mao et al. – Nature

* Influence of excessive exercise on immunity, metabolism and gut microbial diversity in an overtraining mice model – Xin Yuan et al. – Scandinavian Journal of Medicine & Science in Sports

* Mouse: An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin et al. – Genome Biology

* Gut Microbiota-Derived Short Chain Fatty Acids Induce Circadian Clock Entrainment in Mouse Peripheral Tissue – Yu Tahara et al. – Scientific Reports

Time-course responses of ileal and fecal microbiota and metabolite profiles to antibiotics in cannulated pigs – Kan Gao et al. – Applied Microbiology and Biotechnology

Preprint: Toxoplasma gondii infection triggers chronic cachexia and sustained commensal dysbiosis in mice – Jessica A Hatter et al. – bioRxiv

Animal microbiome

Rapid and Specific Methods to Differentiate Foodborne Pathogens, Campylobacter jejuni, Campylobacter coli, and the New Species Causing Spotty Liver Disease in Chickens, Campylobacter hepaticus – Thi Thu Hao Van et al. – Foodborne Pathogens and Disease

Microbial community and short-chain fatty acid profile in gastrointestinal tract of goose – H Yang et al. – Poultry Science

Exploration of the faecal microbiota and biomarker discovery in equine grass sickness – Joy Leng et al. – Journal of Proteome Research

Plant, root and soil microbiome

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad et al. – Environmental Science & Technology

Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata et al. – Letters in Applied Microbiology

Opinion piece: Plant pathogen effector proteins as manipulators of host microbiomes? – Nick C. Snelders et al. – Molecular Plant Pathology

Water and extremophile microbiome

Metabarcoding analysis on European coastal samples reveals new molecular metazoan diversity – David Lopez-Escardo et al. – bioRxiv

Food microbiome

Fungal networks shape dynamics of bacterial dispersal and community assembly in cheese rind microbiomes – Yuanchen Zhang et al. – Nature Communications

Phages and viruses

Distinct Effects of Type I and III Interferons on Enteric Viruses – Harshad Ingle et al. – Viruses

Technology

GC-MS Analysis of Short-Chain Fatty Acids in Feces, Cecum Content, and Blood Samples – Lisa R. Hoving et al. – Clinical Metabolomics

NMR Analysis of Fecal Samples – Hye Kyong Kim et al. – Clinical Metabolomics

Bioinformatics

Spherical: an iterative workflow for assembling metagenomic datasets – Thomas C. A. Hitch and Christopher J. Creevey – BMC Bioinformatics

Microbes in the news

Middle Eastern diet increases gut microbiota diversity, shows benefit in cirrhosis – Healio

Bacterial DNA sequencing could help design ‘friendlier’ nanoparticles – Belle Dumé – Nanotechweb

Consumption of Dietary Fiber May Prevent Metabolic Syndrome – Anamika P – TGHN

Researchers Discover 10 New Immune Systems in Bacteria – Jim Daley – The Scientist

New Ocean-Dwelling, Bacteria-Killing Tailless Virus Hid in Plain Sight – Mindy Weisberger – Live Science

New method developed to detect bacteria in food and water – Ananya Mandal – News Medical

eNose Successfully Recognizes Bacteria in Common Soft Tissue Infections – Michaela Fleming – Contagion Live

Are There Zombie Viruses In The Thawing Permafrost? – Michaeleen Doucleff – NPR

* ‘He was so strong’: Boy, 8, dies from flesh-eating bacteria – by Associated Press – New York Post

Publishing and education

Preprint: Harmonizing semantic annotations for computational models in biology – Maxwell L Neal et al. – bioRxiv

January 25, 2018

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Female sexual and reproductive microbiome: A Bayesian network of the relationship between the vaginal microbiome, habits, demographics and infection risk in reproductive age women, a new mouse model of HIV co-infection demonstrates increased viral shedding in the vagina after gonorrhoeae bacterial infection, and the impacts of diet-induced obesity during pregnancy on the maternal metabolome and gene expression in the placenta in mice.

Water microbiome: How urbanization impact coastal microbiomes, as well as novel organisms from Baltic Sea sediment, and deep-sea hydrothermal vents.

Events and jobs

Clinical Lab Technical Asst Sr – Scripps Health – San Diego CA

Postdoctoral Associate in Soil Health and Water Quality – Stroud Water Research Center – Southeast Pennsylvania

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Human oral microbiome

Review: Salivary biomarkers for oral cancer and pre-cancer screening: a review – J Kaur – Clinical Oral Investigations

Review: In Sickness and in Health—What Does the Oral Microbiome Mean to Us? An Ecological Perspective – P.D. Marsh – Advanced in Dental Research

Therapeutic Strategies Targeting Cariogenic Biofilm Microenvironment – Y. Liu – Advanced in Dental Reserach

Human vaginal microbiome

Review: Probiotics in the Prevention and Treatment of Postmenopausal Vaginal Infections: Review Article – Jun-Mo Kim – Journal of Menopausal Medicine

*Associations between sexual habits, menstrual hygiene practices, demographics and the vaginal microbiome as revealed by Bayesian network analysis – Noelle Noyes – PLOSone

Human gut microbiome

Review: Microbiota-Regulated Outcomes of Human Cancer Immunotherapy via the PD-1/PD-L1 Axis – Jaymin Patel – Biochemistry

Review: Microbiome: Gut microbiota sways response to cancer immunotherapy – Ashley York – Nature Reviews Microbiology

Review: Bacterial Signaling at the Intestinal Epithelial Interface in Inflammation and Cancer – Olivia I. Coleman

Characterization of Fusobacterium varium Fv113-g1 isolated from a patient with ulcerative colitis based on complete genome sequence and transcriptome analysis – Tsuyoshi Sekizuka – PLOSone

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Animal experiments

*Diet-induced obesity alters the maternal metabolome and early placenta transcriptome and decreases placenta vascularity in the mouse – Tami J Stuart – Biology of Reproduction

Gastrointestinal Tract Pathology in a BALB/c Niemann–Pick Disease Type C1 Null Mouse Model – Antony Cougnoux – Digestive Diseases and Sciences

Probiotic/prebiotic correction for adverse effects of iron fortification on intestinal resistance to Salmonella infection in weaning mice  – Feifei Lin – Food and Function

Beneficial effects of consumption of acerola, cashew or guava processing by-products on intestinal health and lipid metabolism in dyslipidaemic female Wistar rats – Kamila Sabino Batista – British Journal of Nutrition

*Neisseria gonorrhoeae co-infection exacerbates vaginal HIV shedding without affecting systemic viral loads in human CD34+ engrafted mice – Stacey X. Xu – PLOSone

Plant, root, and soil microbiome

Interspecific plant interactions reflected in soil bacterial community structure and nitrogen cycling in primary succession – Joseph E. Knelman – Frontiers in Microbiology

Analysis of the succession of structure of the bacteria community in soil from long-term continuous cotton cropping in Xinjiang using high-throughput sequencing – Zhang Wei – Archives of Microbiology

Rhizosphere competence and biocontrol effect of Pseudomonas sp. RU47 independent from plant species and soil type at the field scale – Susanne Schreiter – Frontiers in Microbiology

Estimation of throughfall and stemflow bacterial flux in a subtropical oak-cedar forest – Thais B. Bittar – Geophysical Research Letters

NGS of virus-derived small RNAs as a diagnostic method used to determine viromes of Hungarian vineyards – Nikoletta Czotter – Frontiers in Microbiology

Microbial Remediation of Heavy Metals and Arsenic-Contaminated Environments in the Arid Zone of Northwest China – Xiangliang Pan – In: Luo Y., Tu C. (eds) Twenty Years of Research and Development on Soil Pollution and Remediation in China. Springer, Singapore

Review: Induction of abiotic stress tolerance in plants by endophytic microbes – Rusi Lata – Letters in Applied Microbiology

Amendment of Agricultural Soil with Metal Nanoparticles: Effects on Soil Enzyme Activity and Microbial Community Composition – Bahareh Asadishad – Environmental Science and Technology

Water and extremophile microbiome

*Labilibaculum manganireducens gen. nov., sp. nov. and Labilibaculum filiforme sp. nov., Novel Bacteroidetes Isolated from Subsurface Sediments of the Baltic Sea – Verona Vandieken – Frontiers in Microbiology

*Coastal urbanisation affects microbial communities on a dominant marine holobiont – Ezequiel M. Marzinelli – npj Biofilms and Microbiomes

Microbial Communities and Diversities in Mudflat Sediments Analyzed Using a Modified Metatranscriptomic Method – Yong-Wei Yan – Frontiers in Microbiology

*Novel hydrogenases from deep-sea hydrothermal vent metagenomes identified by a recently developed activity-based screen – Nicole Adam – The ISME Journal

The molecular ecology of Microcystis sp. blooms in the San Francisco Estuary – Timothy G. Otten – Environmental Microbiology

Built environment

Dissertation: Developing Quantitative Abundance Metrics for Microbial Communities – Gabriel Goodney – San Diego State University

Resistome

Antibiotic resistance mutations induced in growing cells of Bacillus-related thermophiles – Hirokazu Suzuki – The Journal of Antibiotics

Food microbiology

A metabolomics study reveals enhanced inhibition and metabolic dysregulation in E. coli induced by Lactobacillus acidophilus fermented black tea extract – Kundi Yang – Journal of Agricultural and Food Chemistry

More Microbes

Environmental Sequencing Fills the Gap Between Parasitic Haplosporidians and Free-living Giant Amoebae – Georgia M. Ward – Eukaryotic Microbiology

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Phages and viruses

Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS91 family insertion sequences – Yuchen Wang – Journal of General Virology

Preprint: Comparative transcriptomics reveals a conserved Bacterial Adaptive Phage Response (BAPR) to viral predation – Bob G. Blasdel – BioRxiv

Bioinformatics

Phylogeny-Based Kernels with Application to Microbiome Association Studies – Jian Xiao – New Advances in Statistics and Data Science

Techniques

Advantages of meta-total RNA sequencing (MeTRS) over shotgun metagenomics and amplicon-based sequencing in the profiling of complex microbial communities – Fabien Cottier – npj Biofilms and Microbiomes

Ecological Stability Properties of Microbial Communities Assessed by Flow Cytometry – Zishu Liu – mSphere

Deconvolution models for a better understanding of natural microbial communities enumerated by flow-cytometry – Gianluca Corno – Cytometry

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Microbes in the news

Bacteria could cause women to give birth prematurely, study finds – Sabrina Barr – Independent

PCOS may reduce gut bacteria diversity – EurekAlert!

Root microbiome valuable key to plants surviving drought – Elaine Smith – Phys.org

Studies in Mice Suggest How Dietary Fiber Reduces Harmful Effects of High-Fat Diet – Genetic Engineering and Biotechnology News

Helicobacter pylori infection permanently changes gastric environment – Medical Press

Dietary Fiber Intake Protects against Diet-Induced Obesity and Metabolic Syndrome – SCI News

The Microbiome of an Oil Reservoir – UC San Diego

Mucin Cross-Feeding Shapes The Metabolic Environment In The Infant Gut – Vera Bunesova – Science Trends

An obesity-associated gut microbiome reprograms the intestinal epigenome and leads to altered colonic gene expression – Yufeng Qin – Genome Biology