Greetings from Chile! Today, in this Digest, a variety of papers covering different subjects, such as the relationships between microbiome and C. difficile infection, new skin microbiome sampling techniques, FMT donor-recipient microbiome interplay, microbiome and biodiversity conservation, microbiome and vitamin metabolism, etc.; also, take a look at the papers from the “Bioinformatics and Microbiome Analysis Techniques” section.  

Human and General Microbiome

A 3D-printed transepidermal microprojection array for human skin microbiome sampling – Kun Liang – PNAS

Analysis of Intestinal Mycobiota of Patients with Clostridioides difficile Infection among a Prospective Inpatient Cohort – Yangchun Cao – Microbiology Spectrum

Role of gastrointestinal microbial populations, a terra incognita of the human body in the management of intestinal bowel disease and metabolic disorders – J E Vazquez Bucheli – Beneficial Microbes

The Gut Bacterial Community Potentiates Clostridioides difficile Infection Severity – Nicholas A Lesniak – mBio

The interplay of gut microbiota between donors and recipients determines the efficacy of fecal microbiota transplantation – Ruiqiao He – Gut Microbes

Gut commensals expand vitamin A metabolic capacity of the mammalian host – Maryam Bonakdar – Cell Host & Microbe

A reappraisal of microbiome dysbiosis during experimental periodontitis – Marion Arce – Molecular Oral Microbiology

Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber – Bryan J Killinger – NPJ Biofilms and Microbiomes

Cooperative action of gut-microbiota-accessible carbohydrates improves host metabolic function – Sawako Tomioka – Cell Reports

Model Animal Microbiome

Key features of the genetic architecture and evolution of host-microbe interactions revealed by high-resolution genetic mapping of the mucosa-associated gut microbiome in hybrid mice – Shauni Doms – eLife

Non-Model Animal Microbiome

Metagenomic insights into the microbe-mediated B and K(2) vitamin biosynthesis in the gastrointestinal microbiome of ruminants – Qian Jiang – Microbiome

Exploring the Transient Microbe Population on Citrus Butterfly Wings – P D Kamala Jayanthi – Microbiology Spectrum

Review: Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter – Júnia Schultz – mSystems

Plant Microbiome

Plant genetic effects on microbial hubs impact host fitness in repeated field trials – Benjamin Brachi – PNAS

Review: Beneficial and pathogenic plant-microbe interactions during flooding stress – Clara Martínez-Arias – Plant, Cell & Environment

Environmental Microbiome

Review: Harnessing the microbiome to prevent global biodiversity loss – Raquel S Peixoto – Nature Microbiology

More Microbes

Proteome Exploration of Legionella pneumophila To Identify Novel Therapeutics: a Hierarchical Subtractive Genomics and Reverse Vaccinology Approach – Md Tahsin Khan – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control – Yingtian Hu – PNAS

A metagenomic DNA sequencing assay that is robust against environmental DNA contamination – Omary Mzava – Nature Communications

Bioinformatic Analysis to Investigate Metaproteome Composition Using Trans-Proteomic Pipeline – Steven He – Current Protocols