Today’s Digest features a major effect to tackle the dark matter in the human gut microbiome, comparison of 8 methods to extract DNA from the oral cavity that yielded an unexpected result, and the investigation on whether we can predict sex/age by our gut microbiota. Enjoy!

General microbiology

Perspective: Bridging the Holistic-Reductionist Divide in Microbial Ecology – Robin Tecon et al. – mSystems

Microbioime sister journal: Welcome to Animal Microbiome – Sharon A. Huws

Engineering microbial consortia by division of labor – Garrett W. Roell et al. – Microbial Cell Factories

Preprint: Revisiting the evolution and taxonomy of Clostridia, a phylogenomic update – Pablo Cruz-Morales et al. – bioRxiv

Human skin microbiome

Skin Microbiota in Contact Sports Athletes and Selection of Antiseptics for Professional Hygiene – Dilyara S. Martykanova et al. – BioMed Research International

Human oral microbiome

Qualitative and quantitative differences in the subgingival microbiome of the restored and unrestored teeth – Steven W. H. Rademacher et al. – Journal of Periodontal Research

Human respiratory microbiome

Comparison of Subtyping Approaches and the Underlying Drivers of Microbial Signatures for Chronic Rhinosinusitis – Kristi Biswas et al. – mSphere

Human gut microbiome

** 1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses – Yuanqiang Zou et al. – Nature Biotechnology

Genomic insights from Monoglobus pectinilyticus: a pectin-degrading specialist bacterium in the human colon – Caroline C. Kim et al. – The ISME Journal

Pinning down the role of common luminal intestinal parasitic protists in human health and disease – status and challenges – Christen Rune Stensvold – Parasitology

Dynamics of the Gut Microbiota in Children Receiving Selective or Total Gut Decontamination Treatment During Hematopoietic Stem Cell Transplantation – Vincent Bekker & Romy D. Zwittink et al. – Biology of Blood and Marrow Transplantation

Fecal Microbiota Transplantation in Patients With Primary Sclerosing Cholangitis: A Pilot Clinical Trial – Jessica Allegretti et al. – The American Journal of Gastroenterology

** Preprint: Age and sex-dependent patterns of gut microbial diversity in human adults – Jacobo de la Cuesta-Zuluaga et al. – bioRxiv

Human reproductive tract microbiome

Cervical microbiota in women with cervical intra-epithelial neoplasia, prior to and after local excisional treatment, a Norwegian cohort study – Johanna Wiik – BMC Women’s Health

Built environment microbiome

Spatial and seasonal variation of the airborne microbiome in a rapidly developing city of China – Hu Li et al. – Science of the Total Environment

Animal experiments

Synbiotic-driven improvement of metabolic disturbances is associated with changes in the gut microbiome in diet-induced obese mice – Xinxin Ke et al. – Molecular Metabolism

The gut microbiota is largely independent of host genetics in regulating fat deposition in chickens – Chaoliang Wen et al. – The ISME Journal

The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome – Nielsen T. Baxter et al. – mSphere

Animal microbiome

Effects of polyethylene microplastics on the gut microbial community, reproduction and avoidance behaviors of the soil springtail, Folsomia candida – Hui Ju et al. – Environmental Pollution

Effects of host blood meal source on reproductive output, nutrient reserves and gut microbiome of West Nile virus vector Culex quinquefasciatus – Aparna Telang & Jessica Skinner – Journal of Insect Physiology

Plant, root and soil microbiome

Soil microbes alter plant fitness under competition and drought – Connor R. Fitzpatrick et al. – Journal of Evolutionary Biology

Multi-resistant plant growth-promoting actinobacteria and plant root exudates influence Cr(VI) and lindane dissipation – María ZoleicaSimón Solá et al. – Chemosphere

Interactions between Pseudomonas spp. and their role in improving the red pepper plant growth under salinity stress – Sandipan Samaddar et al. – Microbiological Research

Plant Defense by VOC-Induced Microbial Priming – Hongwei Liu & Laura E. Brettell – Trends in Plant Science

Water and extremophile microbiome

Microbial ecology of the cryosphere (glacial and permafrost habitats): current knowledge – Rosa Margesin & Tony Collins – Applied Microbiology and Biotechnology

Unique Patterns and Biogeochemical Relevance of Two-Component Sensing in Marine Bacteria – Noelle A. Held et al. – mSystems

Oil-Spill Triggered Shift in Indigenous Microbial Structure and Functional Dynamics in Different Marine Environmental Matrices – C. S. Neethu et al. – Scientific Reports

An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community – Ke Yu et al. – Microbiome

Effects of biomass pyrolysis derived wood vinegar on microbial activity and communities of activated sludge – Fang Zhang et al. – Bioresource Technology

Anti-seasonal submergence dominates the structure and composition of prokaryotic communities in the riparian zone of the Three Gorges Reservoir, China – Yan Fang et al. – Science of The Total Environment

Phages and viruses

Cobaviruses – a new globally distributed phage group infecting Rhodobacteraceae in marine ecosystems – Vera Bischoff et al. – The ISME Journal

In plaque-mass spectrometry imaging of a bloom-forming alga during viral infection reveals a metabolic shift towards odd-chain fatty acid lipids – Guy Schleyer et al. – Nature Microbiology

Technology

The mucosal–luminal interface: an ideal sample to study the mucosa-associated microbiota and the intestinal microbial biogeography – Walid Mottawea et al. – Pediatric Research

Development and application of a HILIC UHPLC-MS method for polar fecal metabolome profiling – Nina Sillner et al. – Journal of Chromatography B

** Evaluation of Oral Cavity DNA Extraction Methods on Bacterial and Fungal Microbiota – Jennifer Rosenbaum et al. – Scientific Reports

Xin’s Non-microbiology pick

Preprint: Where do our graduates go? A toolkit for retrospective and ongoing career outcomes data collection for biomedical PhD students and postdoctoral scholars – Elizabeth A. Silva et al. – bioRxiv