Today’s Digest brings you a comprehensive on microbial recovery after antibiotics, a series of studies in Blood on microbial changes after bone marrow transplant, how global ecological factors can drive soil microbiota evolution, and much more. Enjoy!

General microbiology

Preprint: Horizontal gene transfer drives the evolution of dependencies in bacteria – Akshit Goyal – bioRxiv

Antimicrobial resistance

Cross Journal Series: Health Policy and the Management of Antimicrobial Resistance in LMICs – BMC

** Recovery of the Gut Microbiota after Antibiotics Depends on Host Diet, Community Context, and Environmental Reservoirs – Katharine Michelle Ng et al. – Cell Host & Microbe

Testing sustained soil-to-soil contact as an approach for limiting the abiotic influence of source soils during experimental microbiome transfer – Ryan V Trexler & Terrence H Bell – FEMS Microbiology Letters

Natural products discovery and potential for new antibiotics – Olga Genilloud – Current Opinion in Microbiology

Engineering enzymatic assembly lines to produce new antibiotics – Kenan AJ Bozhüyük et al. – Current Opinion in Microbiology

Human gut microbiome

Antibiotic Exposures and Dietary Intakes Are Associated with Changes in Microbiota Compositions in Allogeneic Hematopoietic Stem Cell Transplant Patients – Chi L. Nguyen et al. – Blood

Impact of Antibiotics on Gut Microbiota Diversity and the Results of a Prospective Dietary Assessment in Patients with Multiple Myeloma Undergoing Autologous Hematopoietic Stem Cell Transplantation – Christopher D’Angelo et al. – Blood

** Impact of Gut Mycobiota Composition on Outcomes after Allogeneic Hematopoietic Cell Transplantation – Florent Malard et al. – Blood

Functional microbiome deficits associated with ageing: Chronological age threshold – Susana Ruiz‐Ruiz et al. – Aging Cell

Human gut-microbiome-brain axis

Review: Gut Microbiota: A Perspective for Psychiatrists – Rea K. et al. – Neuropsychobiology

Metabolomics

Review: Metabolomics biotechnology, applications, and future trends: a systematic review – Qiang Yang et al. – RSC Adv

Animal experiments

Hematopoietic Npc1 mutation shifts gut microbiota composition in Ldlr−/− mice on a high-fat, high-cholesterol diet – Tom Houben et al. – Scientific Reports

Animal microbiome

Cross-kingdom analysis of nymphal-stage Ixodes scapularis microbial communities in relation to Borrelia burgdorferi infection and load – William J Landesman et al. – FEMS Microbiology Ecology

Abdominal microbial communities in ants depend on colony membership rather than caste and are linked to colony productivity – Francisca H. I. D. Segers et al. – Ecology and Evolution

Plant, root and soil microbiome

The invasive potential of a hybrid species: insights from soil chemical properties and soil microbial communities – Feng Sun et al. – Journal of Plant Ecology

** The role of multiple global change factors in driving soil functions and microbial biodiversity – Matthias C. Rillig et al. – Science

Influence of sulfur fertilization on CuO nanoparticles migration and transformation in soil pore water from the rice (Oryza sativa L.) rhizosphere – Lijuan Sun et al. – Environmental Pollution

Water and extremophile microbiome

Effect of temperature on opportunistic pathogen gene markers and microbial communities in long-term stored roof-harvested rainwater – Xiaodong Zhang et al. – Environmental Research

Metabolic profiling of cold adaptation of a deep-sea psychrotolerant Microbacterium sediminis to prolonged low temperature under high hydrostatic pressure – Jin-Mei Xia et al. – Applied Microbiology and Biotechnology

Groundwater cable bacteria conserve energy by sulfur disproportionation – Hubert Müller et al. – The ISME Journal

Bioinformatics

Impact of quality trimming on the efficiency of reads joining and diversity analysis of Illumina paired-end reads in the context of QIIME1 and QIIME2 microbiome analysis frameworks – Attayeb Mohsen et al. – BMC Bioinformatics

Microbes in the news

New Etiology of Rheumatoid Arthritis Identified in the Gut Microbiome – Frieda Wiley – Rheumatology Network

Gut microbiome diversity associates with sleep quality in healthy adults – Allison Clark – Gut Microbiota For Health

Metagenomics Unlocks Unknowns of Diarrheal Disease Cases in Children – John Toon – GA Tech

Clues for predicting premature birth risk may be found in mother’s immune system, microbiome – Amanda Keener – Genetic Literacy Project

Study offers a bird’s eye view of a bird’s smell – Kaylie Connors – Great Lakes Echo

Microbes on the market

Lancôme brings microbiome hub to Hong Kong with DFS – Elena Dimama – DFNI