August 1, 2017

Today’s digest is relatively short, but there is an amazing commentary on rhizosheath and advantages of using phylogenetic distances to examine the microbial communities

Human gut microbiome

Maternal modifiers of the infant gut microbiota: metabolic consequences

Mulligan CM. Journal of Endocrinology

Association between gut microbiota and bone health: potential mechanisms and prospective

Chen YC. The Journal of Clinical Endocrinology & Metabolism

Plant, soil, and air microbiome

Amynthas agrestis invasion increases microbial biomass in Mid-Atlantic deciduous forests

Chang CH. Soil Biology and Biochemistry

Effect of nanoparticles on crops and soil microbial communities

Rajput VD. Journal of Soils and Sediments

Bottom-up effects on herbivore-induced plant defences: a case study based on compositional patterns of rhizosphere microbial communities.

Benítez E. Scientific reports

Unwrapping the rhizosheath

Pang J. Plant and Soil

Marine and inland waters

Marine archaea and archaeal viruses under global change

Danovaro R-F1000 Research

Bacterial community structure in the intertidal biofilm along the Yangtze Estuary, China

Guo X .Marine Pollution Bulletin

Fronts at the surface ocean can shape distinct regions of microbial activity and community assemblages down to the bathypelagic zone: The Azores Front as a case study

Baltar F. Frontiers in Marine Science

Microbiome Approaches/Techniques

A deep metaproteomics approach for the study of human microbiomes

Zhang X Analytical Chemistry, 2017

Advantages of phylogenetic distance based constrained ordination analyses for the examination of microbial communities.

Shankar V. Scientific reports

Oral/Nasal Microbiome 

The periodontal war: microbes and immunity

Ebersole JL. PERIODONTOLOGY 2000

Design and validation of a DNA-microarray for phylogenetic analysis of bacterial communities in different oral samples and dental implants

Parolin C. Scientific Reports

Influence of the pneumococcal conjugate vaccines on the temporal variation of pneumococcal carriage and the nasal microbiota in healthy infants: a longitudinal analysis of a case–control study

Mika M. Microbiome

Food Microbiology 

Comparison study of the volatile profiles and microbial communities of Wuyi Qu and Gutian Qu, two major types of traditional fermentation starters of Hong Qu glutinous rice wine

Liu Z.Food Microbiology

Plant-mediated restriction of Salmonella enterica on tomato and spinach leaves colonized with Pseudomonas plant growth-promoting rhizobacteria

Hsu CK.International Journal of Food Microbiology, 2017

July 21, 2017

Today’s digest is short and sweet. An interesting study of the microbial community composition inside the Internation Space Station using WGS. And, how a microbiologist is saving prairie dogs.

General Microbiome and Microbiology

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology

Carlson H.F1000Research

Animal and insect microbiome

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations

He X. Microbial Ecology

Plant, soil, and air microbiome

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

Abdelfattah A.Biological Control

 Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil

Yuan MM.Global Change Biology

Marine and inland waters

Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland

Jones ZL Applied and Environmental Microbiology

 The effects of phosphorus limitation on carbon metabolism in diatoms

Brembu T. Philosophical  Transaction of the Royal  Society B

Genetic and metabolic engineering in diatoms

Huang W. Philosophical  Transaction of the Royal  Society B

Built Microbiome

Microalgal hydrogen production-a review

Khetkorn W. Bioresource Technology

Whole metagenome profiles of particulates collected from the International Space Station

Nicholas AB.Microbiome, 2017

Microbes in the news

How a wildlife biologist became a plague-chaser in the American Southwest

STAT

17, July 2017

In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

May 28, 2017

Today’s digest includes great reviews on plant-microbe interactions and microbial individual-based ecology (μIBEd).  Lastly, a paper looking at approaches to understanding phage niches.

General Microbiome and Microbiology

Bacterial colonization and succession in a newly opened hospital. Lax S. Science Translational Medicine

Human gut microbiome

Review: Gut microbiota and host defense in critical illness. Jacobs MC. Correct Opinions in Critical Care

Microbiota-gut-brain axis and the central nervous system. Zhu X. Oncotarget

Distinctive microbiomes and metabolites linked with weight loss after gastric bypass, but not gastric banding. Ilhan ZE. ISME Journal

Gut Microbiota: Potential for a Unifying Hypothesis for Prevention and Treatment of Hypertension. Qi Y. Circulation Research

Human microbiome and immune system

Cerebrovascular malformations: Microbiota promotes cerebral cavernous malformations. Ridler C. Nature Review Neurology

Microbiota in T-cell homeostasis and inflammatory diseases. Lee N. Experimental and Molecular Medicine

Microbiota modulation counteracts Alzheimer’s disease progression influencing neuronal proteolysis and gut hormones plasma levels. Bonfili L. Scientific Reports

Animal and insect microbiome

Abiotic and Biotic Factors Regulating Inter-Kingdom Engagement between Insects and Microbe Activity on Vertebrate Remains. Jordan HR. Insects

Microbiome modelling

Review: Advancing microbial sciences by individual-based modelling. Hellweger FL. Nature Reviews Microbiology

Plant, soil, and air microbiome

Ecological effects of soil properties and metal concentrations on the composition and diversity of microbial communities associated with land use patterns in an electronic waste recycling region. Wu W. Science of the Total Environment

Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA. Edwardson CF. ISME Journal

Review: Ancestral alliances: Plant mutualistic symbioses with fungi and bacteria. Martin FM. Science

Review: Dimensions of biodiversity in the Earth mycobiome.Peay GY. Nature Reviews Microbiology

Experimental soil warming shifts the fungal community composition at the alpine treeline. Solly EF. New Phytologist

Virology

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches. Hayes S. Virus

Bacteriophage transfer during faecal microbiota transplantation in <i>Clostridium difficile</i> infection is associated with treatment outcome. Zuo T. Gut Microbiota

May 23, 2017

Today’s microbiome is packed with thought-provoking insights from the status of Microbiology today and in-depth look at what is REALLY in our drinking water.

General Microbiome and Microbiology

Big Questions in Microbiology Mizrahi V. Cell

Human gut microbiome

Uncovering the trimethylamine-producing bacteria of the human gut microbiota. Rath S. Microbiome

The effects of micronutrient deficiencies on bacterial species from the human gut microbiota.Hibberd MC. Science Translational Medicine

Human microbiome and immune system

Potential Impact of Nutrition on Immune System Recovery from Heavy Exertion: A Metabolomics Perspective.Nieman DC. Nutrients

Animal and insect microbiome

Major changes in microbial diversity and community composition across gut sections of a juvenile Panchlora cockroach. Gontang EA. Plus One

A metagenomic approach to discover a novel β-glucosidase from bovine rumensSuwan E. Pure and Applied Chemistry, 2017

Plant, soil, and air microbiome

Tomato root microbiota and Phytophthora parasitica-associated disease. Larousse M. Microbiome

Distance decay relationships in foliar fungal endophytes are driven by rare taxa. Oono R. Environmental Microbiology

Carbon‐driven enrichment of the crucial nitrate reducing bacteria in limed peat soil microcosms. Zhu Y. Letters in applied Microbiology

Using community trait-distributions to assign microbial responses to pH changes and Cd in forest soils treated with wood ash. Cruz-Paredes C. Soil Biology and Biochemistry.

Inland waters and ocean microbiome

Stable microbial communities in the sponge Crambe crambe from inside and outside a polluted Mediterranean harbor.Gantt SE.FEMS Microbiology Letters.

Nutrient stoichiometry shapes microbial community structure in a shallow evaporitic pondLee ZMP.  Frontiers in Microbiology

Impact of drinking water treatment and distribution on the microbiome continuum: an ecological disturbance’s perspective. Zhang Y. Environmental Microbiology

Faecal microbiome 

Changes in microbial ecology after fecal microbiota transplantation for recurrent C. difficile infection affected by underlying inflammatory bowel disease.Khanna S. Microbiome

Probiotics

Antioxidant Properties of Probiotic Bacteria. Wang Y. Nutrients

 STUDYING HOST-MICROBIOTA MUTUALISM USING GNOTOBIOTIC DROSOPHILA. Ma D.Old Herborn University Seminar Monograph 30

Virology

Pre-Symptomatic Diagnosis of Ebola Virus Infection. Navalkar K. Emerging disease and Virology   2017

Succession in the petroleum reservoir microbiome through an oil field production lifecycle.Vigneron A. The ISME Journal

Preprint 

Metabarcoding monitoring analysis: the pros and cons of using co-extracted environmental DNA and RNA data to assess offshore oil production impacts on benthic communities. Laroche O. PeerJ

May 9, 2017

Today’s digest is full of exciting papers that look at how climate change is influencing the gut microbiome of lizards, biogeography of bacteria along the Amazon river, lastly how going to the gym might be bad for you.

Human gut microbiome

Preprint : The Landscape Of Type VI Secretion Across Human Gut Microbiomes Reveals Its Role In Community Composition. Verster A. bioRxiv

Ocean, river, and stream microbiome

Disentangling multi‐scale environmental effects on stream microbial communities. Jyrkänkallio‐Mikkola J. Journal of Biogeography

Bacterial biogeography across the Amazon river-ocean continuum  Doherty M. Frontiers in Microbiology

Spatial variation of microbial communities in sediments along the environmental gradients from Xiaoqing River to Laizhou Bay.   Yu SX.  Marine Pollution Bulletin

The impact of long-term water level draw-down on microbial biomass: A comparative study from two peatland sites with different nutrient status Mpamah PA. European Journal of Soil Biology

The metabolic potential of the single cell genomes obtained from the Challenger Deep, Mariana Trench within the Candidate Superphylum Parcubacteria (OD1). León‐Zayas. Environmental Microbiology

Plant, soil, and air microbiome

Postmortem microbial communities in burial soil layers of skeletonized humans. Thomas TB. Journal of Forensic and Legal Medicine

Metagenomic Analysis of Bacterial Communities in the Rhizosphere of Leguminous Crops and Trees. Ahrenhoerster C. The FASEB Journal

Animal gut microbiome

Can fecal samples be used to inform about microbial communities of the equine hindgut? Reed KJ. Journal of Equine Veterinary Science

Normal variation and changes over time in the equine intestinal microbiome Martin EJ. Journal of Equine Veterinary Science

Climate warming reduces gut microbiota diversity in a vertebrate ectotherm. Bestion E. Nature:Ecology and Evolution

Effect of dietary supplementation with Lactobacillus acidophilus D2/CSL (CECT 4529) on caecum microbioma and productive performance in broiler chickens De Cesare A. PLoS One

Biotechnology 

Editorial Petroleum Microbial Biotechnology: Challenges and Prospects Ismail WA.Frontiers in Microbiology

Antibiotic 

Networks of exchanging antibiotic resistance between environmental, commensal, and pathogenic microbes Dantas G- The FASEB Journal

Extreme environment 

Decoupling of microbial carbon, nitrogen, and phosphorus cycling in response to extreme temperature events Mooshammer M. Science Advances

Faecal microbiome 

pH-Mediated Microbial and Metabolic Interactions in Fecal Enrichment Cultures Ilhan ZE. mSpehere

Anemia During Infancy Affects the Fecal Microbiome and Fecal and Serum Metabolomes McClorry S. The FASEB Journal

Microbes in the news

Southern California beaches get bacteria warnings after rain

Monterey County Herald

The Amount Of Bacteria On Gym Equipment Will Make Sure You Never Forget To Wipe Down The Elliptical Again

Bustle


 

April 20, 2017

Today’s digest is full of interesting articles on the influence of microbes on chronic diseases, and an interesting article on machine learning predictions of soil microbiomes.

Human gut microbiome

The gut microbiota as a modulator of innate immunity during melioidosis. Lankelma JM. PLoS Neglected Tropical Diseases

Apropos: ‘Gut Microbiota Differences in Children From Distinct Socioeconomic Levels Living in the 1 Same Urban Area in Brazil’. Waugh S. Journal of Pediatric Gastroenterology and Nutrition

Review: Microbiota: Diet can protect against type 1 diabetes. Kugelberg E. Nature Review Immunology

Changes in Composition of the Gut Bacterial Microbiome after Fecal Microbiota Transplantation for Recurrent <i>Clostridium difficile</i> Infection in a Pediatric Heart Transplant Patient. Flannigan KL. Frontiers in Cardiovascular Medicine

Understanding the Gut Microbiota in Inflammatory and Functional Gastrointestinal Diseases. Sundin J. Psychosomatic Medicine

Review: Gut Microbiota Modulation and Its Relationship with Obesity Using Prebiotic Fibers and Probiotics: A Review. Dahiya DK. Frontiers in Microbiology

Microbiota, Environment and Diet. de Morais MB. Journal of Pediatric Gastroenterology and Nutrition

Human lung microbiome

Lung Homeostasis: Influence of Age, Microbes, and the Immune System. Lloyd CM. Immunity

Human microbiome and immune system

Homeostatic Immunity and the Microbiota. Belkaid Y. Immunity

Review: Regionalized Development and Maintenance of the Intestinal Adaptive Immune Landscape. Agace WW. Immunity

Human vaginal microbiome

Antimicrobial Compounds Produced by Vaginal <i>Lactobacillus crispatus</i> Are Able to Strongly Inhibit <i>Candida albicans</i> Growth, Hyphal Formation and Regulate Virulence-related Gene Expressions. Wang S. Frontiers of Microbiology

Human liver microbiome 

β-Klotho deficiency protects against obesity through a crosstalk between liver, microbiota, and brown adipose tissue. Somm E. JCI Insight

Animal and insect microbiome

Honeybee gut microbiota promotes host weight gain via bacterial metabolism and hormonal signaling. Zheng H. PNAS.

Comparative Analysis of the Gut Microbial Communities in Forest and Alpine Musk Deer Using High-Throughput Sequencing. Hu X. Frontiers of Microbiology

Mosquito Microbiome Dynamics, a Background for Prevalence and Seasonality of West Nile Virus. Novakova E. Frontiers of Microbiology

Newer Insights into the Antidiarrheal Effects of Acacia catechu Willd. Extract in Guinea Pig.Micucci M. Journal of Medicinal Food

Plant, soil, and air microbiome

Elevated Air Humidity Changes Soil Bacterial Community Structure in the Silver Birch Stand.Truu M. Frontiers of Microbiology

Distance-dependent varieties of microbial community structure and metabolic functions in the rhizosphere of Sedum alfredii Hance during phytoextraction of a cadmium-contaminated soil. Yang W. Environmental science and pollution research

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity. Chang HX. Frontiers of Microbiology

Origin-Dependent Variations in the Atmospheric Microbiome Community in Eastern Mediterranean Dust Storms.Gat D. Environmental science and technology

Faecal microbiome 

Fecal microbiota transplantation is a rescue treatment modality for refractory ulcerative colitis. Uygun A. Medicine (Baltimore)

Probiotics

Mismatch between Probiotic Benefits in Trials versus Food Products. Scourboutakos MJ. Nutrients