December 20, 2019

This may be our last edition of the Microbiome Digest before the holidays kick in. A rich and dynamic Digest brings you all things microbiome (apologies for the tight formatting). An encouraging report on how we can reduce antimicrobial resistance organically, an amazing recovery of a human genome and an oral microbiome from chewed birch pitch thousands of years ago, and a network analysis reveals four levels of hierarchical trophic interactions in the human gut microbiome. Enjoy Reading and Happy Holidays!
Events
BMC Medicine’s upcoming collection, New Frontiers in Diagnosis, Treatment and Management of Neuromuscular Disorders, is soliciting submissions.
Current Issue of The ISME Journal
The 9th Gut Microbiota for Health World Summit – March 7 and 8 2020 in Madrid, Spain
General microbiology
High-order interactions distort the functional landscape of microbial consortia – Sanchez-Gorostiaga & Bajić et al. – PLoS Biology
Antimicrobial resistance
Human skin microbiome
Human oral microbiome
** A 5700 year-old human genome and oral microbiome from chewed birch pitch – Theis Z. T. Jensen et al. – Nature Communications
Press: Ancient “Chewing Gum” Reveals a 5,700-Year-Old Microbiome – Jim Daley – Scientific American
Human respiratory microbiome
Press: Child asthma flare-ups coincide with microbiome changes – JULIA EVANGELOU STRAIT-WUSTL – Futurity
Human gut microbiome
Human vaginal microbiome
Human gut-microbiota-brain axis
Review: Tryptophan Metabolism: A Link Between the Gut Microbiota and Brain – Kan Gao et al. – Advances in Nutrition
Cancer microbiome
Metabolomics
The total microbiome functions in bacteria and fungi – Robert Starke et al. – Journal of Proteomics
Animal experiments
Animal microbiome
Plant, root and soil microbiome
Root microbiomes as indicators of seagrass health – Belinda C Martin et al. – FEMS Microbiology Ecology
Water and extremophile microbiome
Phages and viruses
Technology
Manipulating rod-shaped bacteria with optical tweezers – Zheng Zhang et al. – Scientific Reports
Bioinformatics
** Evidence for a multi-level trophic organization of the human gut microbiome – Tong Wang et al. – PLoS Computational Biology
Microbes in the news
The microbiome is fundamental to both health and disease – Fabian Brockotter – Poultry World
Low FODMAP Diet Helps IDB Patients – Kenny Walter – MDMAG
Oral Health: Caring for the Other Microbiome – Julia Peterman – Whole Foods Magazine
Non-microbiology pick

 

October 9, 2019

Today’s Digest includes plenty of human gut microbiome papers, and plant, soil, water microbiome papers. Today features a major expansion of human gut MAGs, evolution of human gut microbiome compared with apes, and how soil microbiome affects climate change and vice versa. A potentially revolutionary technology promises to finally bring microbiome dark matters into daylight, and don’t forget to check out our own Elies Bik’s excellent work on exposing scientific fraud! Enjoy.

General microbiology

Tradeoffs in hyphal traits determine mycelium architecture in saprobic fungi – Anika Lehmann et al. – Scientific Reports

Review: Nature’s recyclers: anaerobic microbial communities drive crude biomass deconstruction – Stephen P Lillington et al. – Current Opinion in Biotechnology

Review: Microbial functional diversity: From concepts to applications – Arthur Escalas e t al. – Ecology and Evolution

Antimicrobial resistance

Preprint: Discordant bioinformatic predictions of antimicrobial resistance from whole-genome sequencing data of bacterial isolates: An inter-laboratory study – Ronan M Doyle et al. – bioRxiv

Human gut microbiome

** Preprint: A unified sequence catalogue of over 280,000 genomes obtained from the human gut microbiome – Alexandre Almeida et al. – bioRxiv

** Convergence of human and Old World monkey gut microbiomes demonstrates the importance of human ecology over phylogeny – Katherine R. Amato et al. – Genome Biology

Press: New research furthers understanding about what shapes human gut microbiome – EurekAlert!

Review: Sodium, Hypertension, and the Gut: Does the Gut Microbiota Go Salty? – Katarina Smiljanec & Shannon L. Lennon – American Journal of Physiology-Heart and Circulatory Physiology

Tea Compounds and the Gut Microbiome: Findings from Trials and Mechanistic Studies – Timothy Bond & Emma Derbyshire – Nutrients

Fecal microbiota and metabolites are distinct in a pilot study of pediatric Crohn’s disease patients with higher levels of perceived stress – Laura M. Mackner et al. – Psychoneuroendocrinology

Review: The Gut Microbiota in Celiac Disease and probiotics – Richa Chibbar & Levinus A. Dieleman – Nutrients

Systemic Lupus Erythematosus and dysbiosis in the microbiome: cause or effect or both? – Gregg J Silverman et al. – Current Opinion in Immunology

Review: The Multiple Sclerosis Gut Microbiota: A Systematic Review – Ali Mirza et al. – Multiple Sclerosis and Related Disorders

Animal experiments

Oolong tea polyphenols ameliorate circadian rhythm of intestinal microbiome and liver clock genes in mouse model – Tongtong Guo et al. – Journal of Agricultural and Food Chemistry

Review: Caenorhabditis elegans: a model to understand host–microbe interactions – Arun Kumar et al. – Cellular and Molecular Life Sciences

Animal microbiome

Wildlife-microbiome interactions and disease: exploring opportunities for disease mitigation across ecological scales – Candace L. Williams et al. – Drug Discovery Today: Disease Models

Plant, root and soil microbiome

Soil Microbial Communities Involved in Reductive Dissolution of Arsenic from Arsenate-laden Minerals with Different Carbon Sources – Shigeki Yamamura et al. – Environmental Science & Technology

Volatile‐mediated antagonism of soil bacterial communities against fungi – Xiaogang Li et al. – Environmental Microbiology

Interactions between soybean, Bradyrhizobium japonicum and Soybean mosaic virus: the effects depend on the interaction sequence – Sofía Andreola et al. – Functional Plant Biology

New insights into the responses of soil microorganisms to polycyclic aromatic hydrocarbon stress by combining enzyme activity and sequencing analysis with metabolomics – Xiaona Li et al. – Environmental Pollution

Understanding the phyllosphere microbiome assemblage in grape species (Vitaceae) with amplicon sequence data structures – Prashant Singh et al. – Scientific Reports

** Review: Soil microbiomes and climate change – Janet K. Jansson & Kirsten S. Hofmockel – Nature Reviews Microbiology

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Plant-plant competition influences temporal dynamism of soil microbial enzyme activity – E. J. Schofield et al. – Soil Biology and Biochemistry

Comparison of microphototrophic communities living in different soil environments in the High Arctic – Ekaterina Pushkareva et al. – Frontiers in Ecology and Evolution

Water and extremophile microbiome

Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps – Muhammad Farhan Ul Haque et al. – Microbiome

Selective bacterial colonization processes on polyethylene waste samples in an abandoned landfill site – Edoardo Puglisi et al. – Scientific Reports

Variation in pickleweed root-associated microbial communities at different locations of a saline solid waste management unit contaminated with petroleum hydrocarbons – Abdur Rahim Khan et al. – PLoS One

Bacterial and Fungal Diversity Inside the Medieval Building Constructed with Sandstone Plates and Lime Mortar as an Example of the Microbial Colonization of a Nutrient-Limited Extreme Environment (Wawel Royal Castle, Krakow, Poland) – Magdalena Dyda et al. – Microorganisms

Evaluating the effect of biochar on mesophilic anaerobic digestion of waste activated sludge and microbial diversity – Bo Wu et al. – Bioresource Technology

Species-specific differences in the microbiomes and organic exudates of crustose coralline algae influence bacterioplankton communities – Zachary A. Quinlan et al. – Frontiers in Microbiology

A global comparison of the bacterial communities of bilge water, boat surfaces, and external port water – Laura G. Schaerer et al. – Applied and Environmental Microbiology

Microbes in space

Simulated manned Mars exploration: effects of dietary and diurnal cycle variations on the gut microbiome of crew members in a controlled ecological life support system – Hai-Sheng Dong et al. – PeerJ

Technology

** Targeted isolation and cultivation of uncultivated bacteria by reverse genomics – Karissa L. Cross et al. – Nature Biotechnology

Bioinformatics

Tandem repeats lead to sequence assembly errors and impose multi-level challenges for genome and protein databases – Ole K Tørresen et al. – Nucleic Acids Research

Microbes in the news

Bill Gates thinks understanding the body’s microbiome will help solve malnutrition – Katie Palmer – Quartz

Press for yesterday’s article: Unlocking CRISPR’s Potential To Alter the Microbiome – Technology Networks

Press for yesterday’s article: New Study Finds CRISPR May Be The Secret To Improving Gut Health – Gretchen Lidicker – Mind Body Green

Drug Metabolism and Microbiome – Maryam Azizi – News Medical

The Gut-Lupus Link: How Gut Bacteria May Impact Disease Development and Activity – Lupus Foundation of America

Microbes on the market

BASF and Biomillenia Join Forces in Microbiome Research to Promote Healthy Skin – Business Wire

Non-microbiology pick

** Our own Elies Bik is featured in this Dutch report on exposing scientific fraud, and see a Google translated version here.

September 24, 2019

Today’s digest is about diet-microbiota interactions in personalized  nutrition, interesting story on single bacterium association with fatty liver disease and how the gut microbiota adapt to red meat consumption.

General microbiome

Diet–microbiota interactions and personalized nutrition – Aleksandra A. Kolodziejczyk – Nature Reviews Microbiology

Citrobacter rodentium–host–microbiota interactions: immunity, bioenergetics and metabolism – Caroline Mullineaux-Sanders – Nature Reviews Microbiology

The interaction between the gut Microbiota and herbal medicines – Xuedong An – Biomedicine & Pharmacotherapy

Gut microbiota: what is its place in pharmacology? – Aleksandra Tarasiuk – Expert Review of Clinical Pharmacology

Human microbiome

Fatty Liver Disease Caused by High-Alcohol-Producing Klebsiella pneumoniae – Jing Yuan – Cell Metabolism

Association of Alterations in Intestinal Microbiota With Impaired Psychological Function in Patients With Inflammatory Bowel Diseases in Remission – Fabienne Humbel – Clinical Gastroenterology and Hepatology

Butyrate‐Producing Gut Bacteria and Viral Infections in Kidney Transplant Recipients: A Pilot Study – John R. Lee – Transplant Infectious Disease

Metabolomics and Microbial Composition Increase Insight into the Impact of Dietary Differences in Cirrhosis – I. Jane Cox – Liver International

Animal experiments

Gut bacteria responding to dietary change encode sialidases that exhibit preference for red meat-associated carbohydrates – Livia S. Zaramela – Nature Microbiology

A processive endoglucanase with multi-substrate specificity is characterized from porcine gut microbiota – Weijun Wang – Scientific Reports

Comparative analysis of the fecal microbiota from different species of domesticated and wild suids – Florencia Correa-Fiz – Scientific Reports

Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing – Sofiya G. Shevchenko- Applied and Environmental Microbiology

Saponins from Clematis mandshurica Rupr. regulates gut microbiota and its metabolites during alleviation of collagen-induced arthritis in rats – Lin-Xiu Guo – Pharamacological Research

MHC Class II Antigen Presentation by the Intestinal Epithelium Initiates Graft-versus-Host Disease and Is Influenced by the Microbiota – Motoko Koyama – Immunity

Metformin Alters the Duodenal Microbiome and Decreases the Incidence of Pancreatic Ductal Adenocarcinoma Promoted by Diet-induced Obesity – Tien S Dong – American Journal of Physiology

Effects from diet-induced gut microbiota dysbiosis and obesity can be ameliorated by fecal microbiota transplantation: A multiomics approach – Maria Guirro – PlosOne

Short-chain fatty acids and microbiota metabolites attenuate ghrelin receptor signaling – Cristina Torres-Fuentes – Faseb Journal

Effects of berberine and metformin on intestinal inflammation and gut microbiome composition in db/db mice – Wang Zhang – Biomedicine & Pharmacotherapy

Plant, root, soil microbiome

Water-soluble mercury induced by organic amendments affected microbial community assemblage in mercury-polluted paddy soil – Hualing Hu – Chemosphere

Phyllosphere colonisation by a soil Streptomyces sp. promotes plant defense responses against fungal infection – Sophie Vergnes – Molecular Plant-Microbe Interactions

Water microbiome 

Heat‐induced shift in coral microbiome reveals several members of the Rhodobacteraceae family as indicator species for thermal stress in Porites lutea – Wirulda Pootakham – Microbiology Open

Probiotics
Metabolomic profiling of oxalate-degrading probiotic Lactobacillus acidophilus and Lactobacillus gasseri – Casey A. Chamberlain – PlosOne

Probiotic Bifidobacterium bifidum G9‐1 ameliorates phytohemagglutinin‐induced diarrhea caused by intestinal dysbiosis -Yutaka Makizaki – Microbiology and Immunology

July 24, 2019

Welcome back! Today’s all-around Digest features an animal study identifying a single bacterium as therapy against rheumatoid arthritis, a field trial with bacteria colonizing and sterile Asian tiger mosquitoes to combat vector borne diseases, and a non-microbiology pick about the balance between longevity and immunity. Enjoy!

Event

Microbiome Movement – Oncology Response Summit – Boston

General microbiology

Motile curved bacteria are Pareto-optimal – Rudi Schuech et al. – PNAS

Press: ‘Curvy bacteria’ weigh the benefits of different shapes – Science Daily

Antimicrobial resistance

The burden of antimicrobial resistance at tertiary care hospital, southern Ethiopia: a three years’ retrospective study – Tsegaye Alemayehu et al. – BMC Infectious Diseases

Human oral microbiome

Review: Regulation of oral immune tolerance by the microbiome in food allergy – Emmanuel Stephen-Victor & Talal A Chatila – Current Opinion in Immunology

Human respiratory microbiome

Editorial: Changes in lung microbiome do not explain the development of ventilator-associated pneumonia – Lieuwe D. J. Bos & Andre C. Kalil – Intensive Care Medicine

Human gut microbiome

In vitro: Microbial communities in a dynamic in vitro model for the human ileum resemble the human ileal microbiota – Maria Stolaki et al. – FEMS Microbiology Ecology

Fecal Microbiota Transplantation in Pouchitis: Clinical, Endoscopic, Histologic, and Microbiota Results from a Pilot Study – Daniel Selvig et al. – Digestive Diseases and Sciences

Dysbiosis of the gut microbiome is associated with CKD5 and correlated with clinical indices of the disease: a case–controlled study – Yang Li et al. – Journal of Translational Medicine

Animal experiments

Supplementation of diet with non-digestible oligosaccharides alters the intestinal microbiota, but not arthritis development, in IL-1 receptor antagonist deficient mice – Rebecca Rogier et al. – PLoS One

Microbial metabolite deoxycholic acid shapes microbiota against Campylobacter jejuni chicken colonization – Bilal Alrubaye et al. – PLoS One

Lamb: A novel animal model for regional microbial dysbiosis of the pioneer microbial community – Nilusha Malmuthuge and Philip J. Griebel – Frontiers in Microbiology

** A single bacterium restores the microbiome dysbiosis to protect bones from destruction in a rat model of rheumatoid arthritis – Hudan Pan, Ruijin Guo, Yanmei Ju, Qi Wang et al. – Microbiome

Polybrominated Diphenyl Ethers and Gut Microbiome Modulate Metabolic Syndrome–Related Aqueous Metabolites in Mice – David K. Scoville et al. – Drug Metabolism and Disposition

Animal microbiome

** Incompatible and sterile insect techniques combined eliminate mosquitoes – Xiaoying Zheng et al. – Nature

Commentary: Tiger mosquitoes tackled in a trial – Peter Armbruster – Nature

Host genetics and geography influence microbiome composition in the sponge Ircinia campana – Sarah M. Griffiths et al. – Journal of Animal Ecology

Plant, root and soil microbiome

Non-target Effects of Naphthalene on the Soil Microbial Biomass and Bacterial Communities in the Subalpine Forests of Western China – Liying Lan et al. – Scientific Reports

Drought modulates interactions between arbuscular mycorrhizal fungal diversity and barley genotype diversity – Agnieszka Sendek et al. – Scientific Reports

Variation in rhizosphere microbiota correlates with edaphic factor in an abandoned antimony tailing dump – Enzong Xiao et al. – Environmental Pollution

Structural changes of soil organic matter and the linkage to rhizosphere bacterial communities with biochar amendment in manure fertilized soils – Ruilin Huang & Zhenyi Zhang et al. – Science of the Total Environment

Review: The Postharvest Microbiome: The Other Half of Sustainability – Michael Wisniewski & Samir Droby – Biological Control

Water and extremophile microbiome

Oil degradation potential of microbial communities in water and sediment of Baltic Sea coastal area – Hanna Miettinen et al. – PLoS One

Linking dissolved organic matter composition and bacterioplankton communities in an Amazon floodplain system – Michaela L. de Melo et al. – Limnology and Oceanography

Pollution shapes the bacterial community of a river: a case study – N. Yadav & S. Sharma – International Journal of Environmental Science and Technology

A pollution gradient contributes to the taxonomic, functional, and resistome diversity of microbial communities in marine sediments – Jiarui Chen & Shelby E. McIlroy et al. – Microbiome

Phages and viruses

Review: Human Virome and Disease: High-Throughput Sequencing for Virus Discovery, Identification of Phage-Bacteria Dysbiosis and Development of Therapeutic Approaches with Emphasis on the Human Gut – Tasha M. Santiago-Rodriguez & Emily B. Hollister – Viruses

Technology

Targeting 16S rDNA for Stable Recombinant Gene Expression in Pseudomonas – Maike Otto et al. – ACS Synthetic Biology

Microbes in the news

Gut microbes may help malnourished children – Elizabeth Pennisi – Science

The microbiota–gut–brain axis – Natasha Bray – Nature

Nam June Paik Art Center looks at ecosystems, up close – Shim Woo-hyun – The Korea Herald

DuPont Opens State-of-the-Art Probiotics Fermentation Unit – WholeFoods Magazine

The Art Of Solving Antibiotic Overuse in America – ArtIHolics

MICROBIOME RESEARCH IS MORE THAN CHASING GUT FEELINGS – Chad Campbell – Purdue University

NIH grant to fund research on microbiome’s role in cancer – Healio

PET TALK: Balanced GI tract plays large role in dog’s overall well-being – Texas A&M University College of Veterinary Medicine & Biomedical Sciences

Mathematics helps us understand the complexity of our microbiome – Tim Sandle – Digital Journal

Good bacteria, bad products – Gali Weinreb – Globes

Gut Microbiome May Alter ALS Progression in Mice – Julianna LeMieux – GenEngNews

Xin’s non-microbiology pick

** The longevity-promoting factor, TCER-1, widely represses stress resistance and innate immunity – Francis R. G. Amrit et al. – Nature Communications

June 20, 2019

After a week, our Microbiome Digest is back online with a rich collection of articles in all fields microbiome. Highlights include a review on colonization resistance to bacterial pathogens in the gut, a report on daily sampling of the individual microbiome response to similar diets, and, have you heard of the FAIR principles for scientific data? Happy reading!

General microbiology

Bacillus cereus infection in neonates and the absence of evidence for the role of banked human milk: Case reports and literature review – Antoine Lewin et al. – Infection Control & Hospital Epidemiology

Comment: Multiple levels of the unknown in microbiome research – Andrew Maltez Thomas & Nicola Segata – BMC Biology

Comparative genome analysis reveals niche-specific genome expansion in Acinetobacter baumannii strains – Harshita Yakkala & Devyani Samantarrai et al. – PLoS One

Antimicrobial resistance

Definitions and guidelines for research on antibiotic persistence – Nathalie Q. Balaban et al. – Nature Reviews Microbiology

Review: Genomic and metagenomic approaches for predictive surveillance of emerging pathogens and antibiotic resistance – Kimberley V. Sukhum et al. – Clinical Pharmacology & Therapeutics

Review: Antimicrobial Tolerance and Metabolic Adaptations in Microbial Biofilms – Aurélie Crabbé et al. – Trends in Microbiology

Human oral microbiome

Dysbiotic salivary microbiota in dry mouth and primary Sjögren’s syndrome patients – S. Rusthen et al. – PLoS One

Human gut microbiome

** Review: Gut Microbiota and Colonization Resistance against Bacterial Enteric Infection – Q. R. Ducarmon et al. – Microbiology and Molecular Biology Reviews

Review: Gastrointestinal Microbiota in Patients with Chronic Kidney Disease: A Systematic Review – SeonYoon Chung et al. – Advances in Nutrition

Gut Microbial Associations to Plasma Metabolites Linked to Cardiovascular Phenotypes and Risk – Alexander Kurilshikov et al. – Circulation Research

Commentary: The Microbiome, Plasma Metabolites, Dietary Habits, and Cardiovascular Risk Unravelling Their Interplay – Dariush Mozaffarian – Circulation Research

Review: Macronutrient metabolism by the human gut microbiome: major fermentation by-products and their impact on host health – Kaitlyn Oliphant & Emma Allen-Vercoe – Microbiome

Review: Lactose digestion in humans: intestinal lactase appears to be constitutive whereas the colonic microbiome is adaptable – Richard A Forsgård – The American Journal of Clinical Nutrition

** Daily Sampling Reveals Personalized Diet-Microbiome Associations in Humans – Abigail J. Johnson et al – Cell Host & Microbe

Review: HIV, Cancer, and the Microbiota: Common Pathways Influencing Different Diseases – Sergio Serrano-Villar et al. – Frontiers in Immunology

IDDF2019-ABS-0157 Fecal microbiota transplantations reconstitute gut fungal and viral microbiota in graft-versus-host disease – Fen Zhang et al. – Gut

Exploring the impact of Helicobacter pylori on gut microbiome composition – Nihar Ranjan Dash et al. – PLoS One

Metabolomics

Review: Translational Metabolomics: Current Challenges and Future Opportunities – Farhana R. Pinu et al. – Metabolites

Animal experiments

Consumption of post-fermented Jing-Wei Fuzhuan brick tea alleviates liver dysfunction and intestinal microbiota dysbiosis in high fructose diet-fed mice – Xiangnan Zhang et al. – RSC Advance

Mouse: B vitamin sharing promotes stability of gut microbial communities – Vandana Sharma et al. – Frontiers in Microbiology

Variability of the ability of complex microbial communities to exclude microbes carrying antibiotic resistance genes in rabbits – caroline s. achard et al. – Frontiers in Microbiology

Effects of BARLEYmax and high-β-glucan barley line on short-chain fatty acids production and microbiota from the cecum to the distal colon in rats – Seiichiro Aoe et al. – PLoS One

Animal microbiome

The “wildness” of the giant panda gut microbiome and its relevance to effective translocation – Ran Yao & Liangliang Xu et al. – Global Ecology and Conservation

Host genetics influence the rumen microbiota and heritable rumen microbial features associate with feed efficiency in cattle – Fuyong Li et al – Microbiome

Mosquito: Host species and site of collection shape the microbiota of Rift Valley fever vectors in Kenya – David P. Tchouassi et al – PLoS NTD

Longitudinal microbiome profiling reveals impermanence of probiotic bacteria in domestic pigeons – Kirsten Grond, Julie M. Perreau & Wesley T. Loo et al. – PLoS One

Food microbiome

Ground beef microbiome changes with antimicrobial decontamination interventions and product storage – Margaret D. Weinroth et al. – PLoS One

Plant, root and soil microbiome

Biocontrol of Root Diseases and Growth Promotion of the Tuberous Plant Aconitum carmichaelii Induced by Actinomycetes Are Related to Shifts in the Rhizosphere Microbiota – Yulong Li et al. – Microbial Ecology

Microbial communities from different soil types respond differently to organic waste input – Sophie Sadet-Bourgeteau et al. – Applied Soil Ecology

Plant-based oil-sorbents harbor native microbial communities effective in spilled oil-bioremediation under nitrogen starvation and heavy metal-stresses – N. Dashti et al. – Ecotoxicology and Environmental Safety

Effects of agricultural management on rhizosphere microbial structure and function in processing tomato – Jennifer E. Schmidt et al. – Applied and Environmental Microbiology

Microbial diversity in bulk and rhizosphere soil of Ranunculus glacialis along a high-alpine altitudinal gradient – Nadine Praeg et al. – Frontiers in Microbiology

Tripartite Interactions Between Endophytic Fungi, Arbuscular Mycorrhizal Fungi, and Leymus chinensis – Hui Liu et al. – Microbial Ecology

Review: Plant host-associated mechanisms for microbial selection – Piet Jones et al. – Frontiers in Plant Science

Soil Microbial Biomass and Fungi Reduced with Canola Introduced into Long-Term Monoculture Wheat Rotations – Jeremy C. Hansen et al. – Frontiers in Microbiology

Pearls: Microbiota-mediated disease resistance in plants – Nathan Vannier et al. – PLoS Pathogens

Effects of maize rotation on the physicochemical properties and microbial communities of American ginseng cultivated soil – Xiao-Lin Jiao et al. – Scientific Reports

Linking the response of soil microbial community structure in soils to long-term wastewater irrigation and soil depth – Qiuling Dang et al. – Science of the Total Environment

One-time nitrogen fertilization shifts switchgrass soil microbiomes within a context of larger spatial and temporal variation – Huaihai Chen et al. – PLoS One

Water and extremophile microbiome

Comparison of bacterial community structure and potential functions in hypoxic and non-hypoxic zones of the Changjiang Estuary – Dong-Mei Wu & Qiu-Ping Dai et al. – PLoS One

Review: Progress and promise of omics for predicting the impacts of climate change on harmful algal blooms – Gwenn M.M.Hennon & Sonya T.Dyhrman – Harmful Algae

Position-specific metabolic probing and metagenomics of microbial communities reveal conserved central carbon metabolic network activities at high temperatures – Scott C. Thomas et al. – Frontiers in Microbiology

Chemical composition of extracellular polymeric substances and evolution of microbial community in activated sludge exposed to ibuprofen – Guangqing Zhou et al. – Journal of Environmental Management

Enhancement of facultative anaerobic denitrifying communities by oxygen release from roots of the macrophyte in constructed wetlands – Haishu Sun et al. – Journal of Environmental Management

How does environmental inter-annual variability shape aquatic microbial communities? A 40-year annual record of sedimentary DNA from a boreal lake (Nylandssjön, Sweden) – Eric Capo et al. – Frontiers in Ecology and Evolution

Phages and viruses

Review: Virome and bacteriome: two sides of the same coin – Jonathan Stern et al. – Current Opinion in Virology

Technology

Gut microbiome analysis by post: Evaluation of the optimal method to collect stool samples from infants within a national cohort study – Georgina M. Williams et al. – PLoS One

Microbiota data from low biomass milk samples is markedly affected by laboratory and reagent contamination – Josef Dahlberg et al. – PLoS One

Bioinformatics

GRASP2: fast and memory-efficient gene-centric assembly and homolog search for metagenomic sequencing data – Cuncong Zhong et al. – BMC Bioinformatics

Proficiency testing of virus diagnostics based on bioinformatics analysis of simulated in silico high-throughput sequencing datasets – Annika Brinkmann et al. – Journal of Clinical Microbiology

Microbes in the news

FDA recalls certain tattoo inks for bacterial contamination – Fox 13 News

Viruses found to use intricate ‘treadmill’ to move cargo across bacterial cells – ScienceDaily

USDA issues reminder about how to safely meal prep – Erica Chayes Wida – Today

Highlights and key takeaways from the 2019 Boston Bacterial Meeting (BBM) – Dr. Tomislav Meštrović, MD, Ph.D. – News Medical

Non-microbiology picks

** The State of Open Data Report 2018

Network analysis to evaluate the impact of research funding on research community consolidation – Daniel J. Hicks et al. – PLoS One

June 4, 2019

General microbiome
Rigorous Statistical Methods for Rigorous Microbiome Science – Amy D. Willis – mSystems

Understanding microbial community dynamics to improve optimal microbiome selection – Robyn J. Wright – Microbiome

Toward a Better Understanding of Species Interactions through Network Biology – Ryan S. McClure – mSystems

Human respiratory microbiome
Nasal commensal Staphylococcus epidermidis enhances interferon-λ-dependent immunity against influenza virus – Hyun Jik Kim – Microbiome

Human gut microbiome
A Multi-omics Approach to Unraveling the Microbiome-Mediated Effects of Arabinoxylan Oligosaccharides in Overweight Humans – Alfonso Benítez-Páez – mSystems

Gut microbiome identifies risk for colorectal polyps – Ezzat Dadkhah – BMJ Open Gastroenterology

Yogurt improves insulin resistance and liver fat in obese women with nonalcoholic fatty liver disease and metabolic syndrome: a randomized controlled trial – Yang Chen – American Journal of Clinical Nutrition

Preprint: Chemical Impacts of the Microbiome Across Scales Reveal Novel Conjugated Bile Acids – Robert A Quinn – bioRxiv

Animal models
Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model – Limei Lin – Microbiome

Missing Links: the Role of Primates in Understanding the Human Microbiome – Katherine R. Amato – mSystems

Plant, root, and soil microbiome
Collaborative involvement of woody plant roots and rhizosphere microorganisms in the formation of pedogenetic clays – Frank Reith – Annals of Botany

Water and extremophile microbiome
Effects of sulfamethoxazole and sulfamethoxazole-degrading bacteria on water quality and microbial communities in milkfish ponds – Bea-Ven Chang – Environmental Pollution

Preprint: Temporal dynamics of Bacteria, Archaea and protists in equatorial coastal waters – Caroline Chénard – bioRxiv

Built environment
Concurrent measurement of microbiome and allergens in the air of bedrooms of allergy disease patients in the Chicago area – Miles Richardson – Microbiome

Phages and viruses
Preprint: The human gut virome is highly diverse, stable and individual-specific – Andrey Shkoporov – bioRxiv

Bioinformatics
NG-meta-profiler: fast processing of metagenomes using NGLess, a domain-specific language – Luis Pedro Coelho – Microbiome

Science, publishing, and career
Preprint: The Mastery Rubric for Bioinformatics: supporting design and evaluation of career-spanning education and training – Rochelle E. Tractenberg – bioRxiv

Alyson’s non-microbiology picks
Why Your Metro Commute Is So Insanely Windy – Julie Bogen – The Atlantic

The 2019 Wellcome photography prize: close focus on the human condition – Sean O’Hagan – The Guardian

April 29, 2019

Today’s Monday morning digest is about correlations of human gut microbiome with circulating metabolites, coronary artery disease severity; microbial communities in biogas plants, and proteomic profiling of gut microbiota-associated bile salt hydrolase activity.

Human gut microbiome

Correlation of Gut Microbiome Between ASD Children and Mothers and Potential Biomarkers for Risk Assessment – Ning Li – Genomics, Proteomics & Bioinformatics

Neonatal Vitamin A Supplementation and Vitamin A Status Are Associated with Gut Microbiome Composition in Bangladeshi Infants in Early Infancy and at 2 Years of Age – M Nazmul Huda – Journal of Nutrition

Diversification and evolution of vancomycin-resistant Enterococcus faecium during intestinal domination – Krista A. Dubin – Infection and Immunity

Microbiota as a cornerstone in the development of primary sclerosing cholangitis: paving the path for translational diagnostic and therapeutic approaches – Catherine Mooser – Gut

Alterations in the gut microbiome and metabolism with coronary artery disease severity – Honghong Liu – Microbiome

Deciphering the complex interplay between microbiota, HPV, inflammation and cancer through cervicovaginal metabolic profiling – Zehra Esra Ilhan – EBio Medicine

Relationship between gut microbiota and circulating metabolites in population-based cohorts – Dina Vojinovic – BioRxiv

Animal experiments

Antibiotics-induced perturbations in gut microbial diversity influence metabolic phenotypes in a murine model of high-fat diet-induced obesity – Dongmin Liu – Applied Microbiology and Biotechnology

Composition, diversity and function of gastrointestinal microbiota in wild red-billed choughs (Pyrrhocorax pyrrhocorax) – Wen Wang – International Microbiology

Plant, root, soil microbiome

Antioxidant activity changes of exopolysaccharides with different carbon sources from Lactobacillus plantarum LPC-1 and its metabolomic analysis – Xin Cheng – World Journal of Microbiology and Biotechnology

Effects of grassland afforestation on structure and function of soil bacterial and fungal communities – Kaibo Wang – Science of the Total Environment

Water microbiome and extremophiles

Effect of applied voltage and temperature on methane production and microbial community in microbial electrochemical anaerobic digestion systems treating swine manure – Jaecheul Yu – Journal of Industrial Microbiology & Biotechnology

Metaproteome analysis reveals that syntrophy, competition, and phage-host interaction shape microbial communities in biogas plants – R. Heyer – Microbiome

Techniques

Improving Assignment of Microbial Genetic Polymorphisms Assignments in Complex Samples by Bayesian Estimation – Jiarui Li – Genomics, Proteomics & Bioinformatics

Accounting for Biological Variation With Linear Mixed-effects Modelling Improves the Quality of Clinical Metabolomics Data – Kwanjeera Wanichthanarak – Computational and Structural Biotechnology Journal

Chemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity – Bibudha Parasar – ACS Central Science

Microbiome in news

Human Microbiome Therapeutics Market Research Methodology- Prominent Players Enterome Bioscience, Yakult Honsha Co. Ltd., DuPont – The Market Bureau

The Week That Wasn’t: See-Through Skulls, Fecal Soup, Microbiome Pill – Medscape

Non-Microbiology Picks

The incretin system in healthy humans: the role of GIP and GLP-1 – Jens Juul Holst – Metabolism