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.
Microbiome Digest - Bik's Picks 