Sorry for the late afternoon digest. We are in the midst of trying to get our lab back up and running! There are several interesting papers today, including a commentary on the holobiont model and the usefulness of integrating microbiome and GWAS data, the development of a “Microbiome-Derived Metabolism Screen” for personalized medicine published in Cell, and a paper investigating phylosymbiosis in the skin microbiome of fish. My non-microbiology pick is a urine sampling method to assess diet, which could be very useful to gut microbiome scientists.

General microbiome

Commentary: Re-evaluating the relationship between missing heritability and the microbiome – Gavin M. Douglas – Microbiome

Book chapter: Pharmacomicrobiomics – Weihua Huang – Pharmacogenomics in Precision Medicine

Human gut microbiome

Review: Altered Composition of Gut Microbiota in Depression: A Systematic Review – Zahra Amirkhanzadeh Barandouzi – Frontiers in Psychiatry

Review: Tryptophan Metabolites Along the Microbiota-Gut-Brain Axis: An Interkingdom Communication System Influencing the Gut in Health and Disease – Annalisa Bosi – International Journal of Tryptophan Research

Personalized Mapping of Drug Metabolism by the Human Gut Microbiome – Bahar Javdan – Cell

Bacteroides thetaiotaomicron-derived outer membrane vesicles promote regulatory dendritic cell responses in health but not in inflammatory bowel disease – Lydia Durant – Microbiome

Animal microbiome

The skin microbiome of elasmobranchs follows phylosymbiosis, but in teleost fishes, the microbiomes converge – Michael P. Doane – Microbiome

Whole-genome sequence analysis of environmental Escherichia coli from the faeces of straw-necked ibis (Threskiornis spinicollis) nesting on inland wetlands – Ethan R Wyrsch – Microbial Genomics

Intestinal Microbiota Analyses of Litopenaeus vannamei During a Case of Atypical Massive Mortality in Northwestern Mexico – Alejandro López-Cortés – Current Microbiology

Identification of hepatitis C virus in the common bed bug–a potential, but uncommon route for HCV infection? – Jiaxin Ling – Emerging Microbes & Infections

Eggshell and environmental bacteria contribute to the intestinal microbiota of growing chickens – Joel J. Maki – Journal of Animal Science and Biotechnology

Topography of the respiratory tract bacterial microbiota in cattle – Christopher McMullen – Microbiome

Plant, root, and soil microbiome

Exploring slope spatial heterogeneity by nitrogen transfer and arbuscular mycorrhizal community – Yanyan Yu – Journal of Soils and Sediments

Disentangling drivers of soil microbial potential enzyme activity across rain regimes: An approach based on the functional trait framework – Gabin Piton – Soil Biology and Biochemistry

Microbial communities in petroleum-contaminated seasonally frozen soil and their response to temperature changes – Xusheng Wang – Chemosphere

Review: The Plant Microbiome: From Ecology to Reductionism and Beyond – Connor R. Fitzpatrick – Annual Review of Microbiology

Biogeographic patterns of microbial co-occurrence ecological networks in six American forests – Qichao Tu – Soil Biology and Biochemistry

Water, air, and extremophile microbiome

Microbial communities of container aquatic habitats shift in response to Culex restuans larvae – Ephantus J. Muturi – FEMS Microbiology Ecology

Climate mediates continental scale patterns of stream microbial functional diversity – Félix Picazo – Microbiome

Bacterial diversity of a high-altitude permafrost thaw pond located on Ojos del Salado (Dry Andes, Altiplano-Atacama region) – Júlia Margit Aszalós – Astrobiology  

Effects of active volcanism on bacterial communities in the highest-altitude crater lake of Ojos del Salado (Dry Andes, Altiplano-Atacama Region) – Júlia Margit Aszalós – Astrobiology  

Methanogenesis in the Lake Elton saline aquatic system – Anna Kallistova – Extremophiles

Auxotrophic interactions: A stabilizing attribute of aquatic microbial communities? – Winifred Johnson – FEMS Microbiology Ecology

Food microbiology

Lactic acid accumulation under heat stress related to accelerated glycolysis and mitochondrial dysfunction inhibits the mycelial growth of Pleurotus ostreatus – Zhiyu Yan – Applied Microbiology and Biotechnology

Evaluation and comparison of the microbial communities and volatile profiles in homemade suansun from Guangdong and Yunnan provinces in China – Qianqian Guan – Journal of the Science of Food and Agriculture

Non-Microbiology Pick

Developing community-based urine sampling methods to deploy biomarker technology for the assessment of dietary exposure – Amanda J. Lloyd – Public Health Nutrition