Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more.

Also, you can support the outreachy bugsigdb project by sharing your study to be curated (more info here https://www.outreachy.org/apply/project-selection/#bioconductor or contact me). See you at #MVIF next week!

Week 2: we're looking for #microbiome papers to curate!

If you published work w/differential & taxonomy analysis & would love to be in #bugsigsdb, an open source (community-editable!) of microbial signatures, just DM me!@outreachy applicants will be happy to curate your study!

— Svetlana U. Perović (@svetlana_up) October 10, 2023

General

From hype to hope: considerations in conducting robust microbiome science – Amelia J McGuinness – Brain, Behavior, and Immunity

Global

Unraveling the functional dark matter through global metagenomics – Georgios A. Pavlopoulos – Nature

Human gut microbiome

Integration of 168,000 samples reveals global patterns of the human gut microbiome – Richard J. Abdill – bioRxiv

Analysis of strain, sex, and diet-dependent modulation of gut microbiota reveals candidate keystone organisms driving microbial diversity in response to American and ketogenic diets – Anna C. Salvador – Microbiome

Gut microbial genomes with paired isolates from China signify probiotic and cardiometabolic effects – Pan Huang – bioRxiv

Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index – Sofía Tesolato – PlosOne

Tracking gut microbiome and bloodstream infection in critically ill adults – Christopher H. Gu – PlosOne

Human milk

Human milk oligosaccharides modify the strength of priority effects in the Bifidobacterium community assembly during infancy – Martin F. Laursen & Henrik M. Roager – The ISME Journal

Antibiotic Resistome

Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments – Jessica Subirats – Applied and Environmental Microbiology

Plant microbiome

Characterization of Differences of Seed Endophytic Microbiome in Conventional and Organic Rice by Amplicon-based Sequencing and Culturing Methods – Sabin Khana – bioRxiv

Animal microbiome

Microbiome species diversity and seasonal stability of two temperate marine sponges Hymeniacidon perlevis and Suberites massa – Claire E. Lamb & Joy E. M. Watts – Environmental Microbiome

An observational study of the presence and variability of the microbiota composition of goat herd milk related to mainstream and artisanal farm management – Rita A. H. Hoving-Bolink – PlosOne

Technique

Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers – Oona L.O. Snoeyenbos-West – bioRxiv

Our latest lab paper led by @ElectricBiome . We tested new cute little plate readers in the anaerobic chamber and present out results and experience using them. They’re affordable and could easily fit 2-4 of them is a 2-person COY chamber. https://t.co/2wgoi4FaGo

— 𝙋𝙖𝙪𝙡 𝘾𝙖𝙧𝙞𝙣𝙞 (@Paul_Carini) October 11, 2023

Bioinformatics

On the relationship between protist metabarcoding and protist metagenome-assembled genomes – Daryna Zavadska – bioRxiv

Track, Analyze, Visualize: Unravel Your Microbiome’s Temporal Tale with MicrobiomeStat – Chen Yang & MicrobiomeStat team

The FULL program w/ abstracts for #MVIF #22 is OUT https://t.co/brHZE8qmTQ

⭐️ Keynote:
🇦🇺 @linsalrob (@Flinders)

⭐️ Selected talks:
🇨🇦 Courtney Hoskinson @TurveyLab
🇺🇸 @avcarrology
🇸🇬 @minghao_chia

⭐️ Highlights:
🇵🇭 Aldwin Adiong (@Official_UPD)
🇮🇳Deep Chanda (@NITDgp1955) pic.twitter.com/KzaL5AGDOq

— Microbiome Virtual International Forum (@MicrobiomeVIF) October 7, 2023