August 10, 2022

General microbiome

Microbiome-associated human genetic variants impact phenome-wide disease risk – Markowitz et al. – PNAS

Microbial risk score for capturing microbial characteristics, integrating multi-omics data, and predicting disease risk – Wang et al. – Microbiome

[REVIEW]A framework for testing the impact of co-infections on host gut microbiomes – Schmid et al. – Animal Microbiome

Human vaginal microbiome

Vaginal microbiota and personal risk factors associated with HPV status conversion—A new approach to reduce the risk of cervical cancer? – Yang et al. – PLOS One

Human gut microbiome

[REVIEW]The role of the gut microbiota in multiple sclerosis – Correale, Hohlfeld & Baranzini

Specific gut microbiota alterations in essential tremor and its difference from Parkinson’s disease – Zhang et al. – NPJ Parkinson’s Disease

Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics – Podlesny et al. – Cell Reports Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Cheung et al. – Journal of Gastroenterology and Hepatology

Targeted suppression of human IBD-associated gut microbiota commensals by phage consortia for treatment of intestinal inflammation – Federici et al. – Cell

Animal microbiome

Camel milk microbiota: A culture-independent assessment – Rahmeh et al. – Food Research International

Effect of processing on the anti-inflammatory efficacy of cocoa in a high fat diet-induced mouse model of obesity – Weikart et al. – The Journal of Nutritional Biochemistry

The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs – Gaire et al. – Microbiome

Plant, root, and soil microbiome

Soil microbial community structures are shaped by agricultural systems revealing little temporal variation – Fox, Widmer & Lüscher – Environmental Research

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

The streamwater microbiome encodes hydrologic data across scales – URycki et al. – Science of The Total Environment

Bioinformatics / Data

[PREPRINT]Lake iTag measurements over nineteen years, introducing the limony dataset – Rohwer & McMahon – bioRxiv

August 03, 2022

Pregnancy and early life

The abundance of Ruminococcus bromii is associated with faecal butyrate levels and atopic dermatitis in infancy – Sasaki et al. – Allergy

Human oral microbiome

Smokeless tobacco consumption induces dysbiosis of oral mycobiome: a pilot study – Sajid et al. – Applied Microbiology and Biotechnology

Human gut microbiome

The Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron In Vivo Is Influenced by Environmental and Host-Derived Factors – Stentz et al. – Applied and Environmental Microbiology

Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains – FitzGerald et al. – Gut Microbes

[REVIEW]Targeting microbiota-host interactions with resveratrol on cancer: Effects and potential mechanisms of action – Wang et al. – Critical Reviews in Food Science and Nutrition

Emerging frontiers of antibiotics use and their impacts on the human gut microbiome – Kumari et al. – Microbiological Research

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Microbiota of the Pregnant Mouse: Characterization of the Bacterial Communities in the Oral Cavity, Lung, Intestine, and Vagina through Culture and DNA Sequencing – Greenberg et al. – Microbiology Spectrum

Phages and viruses

Viral biogeography of the mammalian gut and parenchymal organs – Shkoporov – Nature Microbiology

Bioinformatics

Namco: a microbiome explorer – Dietrich et al. – Microbial Genomics

MiCloud: A unified web platform for comprehensive microbiome data analysis – Gu et al. – PLOS One

July 26, 2022

Highlights!

Microbial determinants of effective donors in faecal microbiota transplantation for UC – Craig Haifer – Gut → Metagenomic and metabolomic data analysis showed that donor microbiota stability and increased species evenness were identified novel markers associated with donor sample therapeutic efficacy in Ulcerative Colitis.

A gut microbial peptide and molecular mimicry in the pathogenesis of type 1 diabetes – Khyati Girdhar – PNAS → A peptide sequence from Parabacteroides distasonis mimics an important insulin epitope, making it susceptible to generating type I diabetes in a mouse model. 

Human and General Microbiome

Gut microbiome changes in anti-N-methyl-D-aspartate receptor encephalitis patients – Jingya Wei – BMC Neurology

Effect of a bacteriocin-producing Streptococcus salivarius on the pathogen Fusobacterium nucleatum in a model of the human distal colon – Garreth W Lawrence – Gut Microbes

Identification of Gut Microbiome Metabolites via Network Pharmacology Analysis in Treating Alcoholic Liver Disease – Ki-Kwang Oh – Current Issues in Molecular Biology

Review: The Gut Microbiota: A Double Edge Sword in Endometriosis – Chandni Talwar – Biology of Reproduction

Non-Model Animal Microbiome

Hair Microbiome Diversity within and across Primate Species – Catherine Kitrinos – mSystems

Seasonal variations in the composition and diversity of gut microbiota in white-lipped deer (Cervus albirostris) – Zhangqiang You – PeerJ

Plant Microbiome

Effects of Domestication on Plant-Microbiome Interactions – Andres Gutierrez – Plant & Cell Physiology

Evaluation of protein extraction methods for metaproteomic analyses of root-associated microbes – Fernanda Salvato – Molecular Plant-Microbe Interactions

Environmental Microbiome

Absence of stress-promoted facilitation coupled with a competition decrease in the microbiome of ephemeral saline lakes – Mateu Menéndez-Serra – Ecology

Insights into the Antimicrobial Activities and Metabolomes of Aquimarina (Flavobacteriaceae, Bacteroidetes) Species from the Rare Marine Biosphere – Sandra Godinho Silva – Marine Drugs

More microbes

Correspondence: International travel, the gut microbiome, and ESBL-E coli carriage – Ye Peng – The Lancet. Microbe

An Engineered λ Phage Enables Enhanced and Strain-Specific Killing of Enterohemorrhagic Escherichia coli – Menglu Jin – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

MOCHI, a comprehensive cross-platform tool for amplicon-based microbiota analysis – Jun-Jie Zheng – Bioinformatics

July 23, 2022

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

July 16, 2022

Human and General Microbiome

Advances and challenges in cataloging the human gut virome – Junhua Li – Cell Host & Microbe

Genomic diversity of genus Limosilactobacillus – Magdalena Ksiezarek – Microbial Genomics

Comparison of the respiratory tract microbiome in hospitalized COVID-19 patients with different disease severity – Jiali Chen – Journal of Medical Virology

An international report on bacterial communities in esophageal squamous cell carcinoma – Jason Nomburg – International Journal of Cancer

Beneficial Microbes and Compounds

Phenolic-rich beverages reduce bacterial TMA formation in an ex vivo-in vitro colonic fermentation model – Lisard Iglesias-Carres – Food & Function

Lactobacillus paragasseri OLL2809 Improves Depression-Like Behavior and Increases Beneficial Gut Microbes in Mice – Narumi Hashikawa-Hobara – Frontiers in Neuroscience

In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus – Linda B Oyama – NPJ Biofilms and Microbiomes

Review: How Dietary Fibre, Acting via the Gut Microbiome, Lowers Blood Pressure – Chudan Xu – Current Hypertension Reports

Review: Low FODMAP diet in irritable bowel syndrome: a review of recent clinical trials and meta-analyses – Kevin Whelan – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Prebiotic effects of plant-derived (poly)phenols on host metabolism: Is there a role for short-chain fatty acids? – Perla Lopes de Freitas – Critical Reviews in Food Science and Nutrition

Animal Microbiome

Unveiling biogeographic patterns in the worldwide distributed Ceratitis capitata (medfly) using populations genomics and microbiome composition – María Belén Arias – Molecular Ecology

Differential oral microbiome in nonhuman primates from periodontitis susceptible and resistant matrilines – Jeffrey L Ebersole – Molecular Oral Microbiology

Chicken jejunal microbiota improves growth performance by mitigating intestinal inflammation – Xiaolong Zhang – Microbiome

Bioinformatics and Microbiome Analysis

Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing – Lei Zhang – Frontiers in Cellular and Infection Microbiology

KOMB: K-core based de novo characterization of copy number variation in microbiomes – Advait Balaji – Computational and Structural Biotechnology Journal

CASPER: An Integrated Software Platform for Rapid Development of CRISPR Tools – Brian Mendoza – The CRISPR Journal

Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study – Qiang Zeng – Frontiers in Endocrinology

July 13, 2022

Today’s digest features studies on the leaf-microbiome of 🍅 and 🍓 plants (+ bumblebees and mites), human gut and wastewater resistome, and more. Happy reading!

Reproductive tract

Female reproductive tract microbiota and recurrent pregnancy loss: a nested case-control study – Pirkko Peuranpää – Reproductive BioMedicine Online

Gut microbiome

Dynamic metabolic interactions and trophic roles of human gut microbes identified using a minimal microbiome exhibiting ecological properties – Sudarshan A. Shetty – Journal of the International Society for Microbial Ecology

*Within-patient evolution of plasmid-mediated antimicrobial resistance – Javier DelaFuente – bioRxiv

An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species – Sigal Leviatan – Nature Communications

Animal microbiome

Carpenter Bees (Xylocopa) Harbor a Distinctive Gut Microbiome Related to That of Honey Bees and Bumble Bees – Jo-anne C. Holley – Applied and Environmental Microbiology

Animal experiments

Gardnerella Exposures Alter Bladder Gene Expression and Augment Uropathogenic Escherichia coli Urinary Tract Infection in Mice – Nicole M. Gilbert – Frontiers in Cellular and Infection Microbiology

Plant microbiome

*The Greenhouse Phyllosphere Microbiome and Associations with Introduced Bumblebees and Predatory Mites – Marie Legein – Microbiology Spectrum

Food microbiome

Longitudinal, multi-platform metagenomics yields a high-quality genomic catalog and guides an in vitro model for cheese communities – Christina C. Saak – bioRxiv

New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria – Muhammad Yasir – Food Research International

Water microbiome

*High-resolution characterisation of short-term temporal variability in the taxonomic and resistome composition of wastewater influent – Kevin Kaibond Chau – bioRxiv

Pilot investigation on biostability of drinking water distribution systems under water source switching – Kejia Zhang – Applied Microbiology and Biotechnology

Bioinformatics

*BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes – Michael J. Pavia – bioRxiv

getSequenceInfo: a suite of tools allowing to get genome sequence information from public repositories – Vincent Moco – BMC Bioinformatics

baseLess: Lightweight detection of sequences in raw MinION data – Ben Noordijk – bioRxiv

July 12, 2022

Human and General Microbiome

Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections – Paula Hayakawa Serpa – Genome Medicine

Alterations in gut microbiota of esophageal squamous cell carcinoma patients – Man Kit Cheung – Journal of Gastroenterology and Hepatology

Altered Pattern of Immunoglobulin A-Targeted Microbiota in Inflammatory Bowel Disease After Fecal Transplantation – Wen-Qi Huang – Frontiers in Microbiology

16S rRNA gene sequencing reveals an altered composition of gut microbiota in children with Mycoplasma pneumoniae pneumonia treated with azithromycin – Qiong Deng – The Journal of General and Applied Microbiology

Clinical and metagenomic profiling of hormonal acne-prone skin in different populations – Nina Hrapovic – Journal of Cosmetic Dermatology

Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury – Cristina Rodriguez-Diaza – Pharmacological Research

Beneficial Microbes and Compounds

Review: The potential role of prebiotics, probiotics, and synbiotics in adjuvant cancer therapy especially colorectal cancer – Zahoor Alam – Journal of Food Biochemistry

Review: Probiotics, prebiotics and postbiotics for better sleep quality: a narrative review – J E Haarhuis – Beneficial Microbes

Review: Gut Microbiota: A Novel Therapeutic Target for Parkinson’s Disease – Manlian Zhu – Frontiers in Immunology

Animal Model Microbiome

Obesity enriches for tumor protective microbial metabolites and treatment refractory cells to confer therapy resistance in PDAC – Kousik Kesh – Gut Microbes

Profiling of d-alanine production by the microbial isolates of rat gut microbiota – Cindy J. Lee – The FASEB Journal

Non-Model Animal Microbiome

Within-community variation of interspecific divergence patterns in passerine gut microbiota – Jan Kubovčiak – Ecology and Evolution

Bacteriophages

Phage defence by deaminase-mediated depletion of deoxynucleotides in bacteria – Brian Y. Hsueh – Nature Microbiology

Bioinformatics and Microbiome Analysis

Preprint: CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning – Alex Chklovski – biorXiv

Cancer type classification using plasma cell-free RNAs derived from human and microbes – Shanwen Chen – eLife

Temporal Alignment of Longitudinal Microbiome Data – Ran Armoni – Frontiers in Microbiology

A Bottom-up Approach to Testing Hypotheses That Have a Branching Tree Dependence Structure, with Error Rate Control – Yunxiao Li – Journal of the American Statistical Association

July 9, 2022

Have a nice weekend! 

Human and General Microbiome

Review: Bladder cancer, inflammageing and microbiomes – Austin Martin – Nature Reviews. Urology

Review: Gut associated metabolites and their roles in Clostridioides difficile pathogenesis – Andrea Martinez Aguirre – Gut Microbes

Oral and gut dysbiosis leads to functional alterations in Parkinson’s disease – Sungyang Jo – NPJ Parkinson’s Disease

Transcriptional programming in a Bacteroides consortium – Brian D Huang – Nature Communications

Gut microbiota composition in colorectal cancer patients is genetically regulated – Francesca Colombo – Scientific Reports

Relative contributions of the host genome, microbiome, and environment to the metabolic profile – Kangjin Kim – Genes & Genomics

Beneficial Microbes and Compounds

Effects of probiotic Lactiplantibacillus plantarum IMC 510 supplementation on metabolic factors in otherwise healthy overweight and obese individuals – Maria Magdalena Coman – Journal of Applied Microbiology

Grape seed and skin extract, a potential prebiotic with anti-obesity effect through gut microbiota modulation – Mohamed Mokrani – Gut Pathogens

Lactobacillus acidophilus LA85 ameliorates cyclophosphamide-induced immunosuppression by modulating Notch and TLR4/NF-κB signal pathways and remodeling the gut microbiota – Liangyu Xue – Food & Function

Animal Model Microbiome

Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis – Anshul Sinha – Microbiome

Non-Model Animal Microbiome

Rickettsia helvetica infection is associated with microbiome modulation in Ixodes ricinus collected from humans in Serbia – Apolline Maitre – Scientific Reports

Environmental Microbiome

Microplastic exposure across trophic levels: effects on the host-microbiota of freshwater organisms – Javier Edo Varg – Environmental Microbiome

Estuarine plastisphere as an overlooked source of N(2)O production – Xiaoxuan Su – Nature Communications

Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics – Joon-Yong Lee – Journal of Proteome Research

Other

Privacy Risks in Microbiome Research: Public Perspectives before and during a Global Pandemic – Andrea Shin – Ethics & Human Research

Bioinformatics and Experimental Microbiome Analysis

Review: Metagenomics Approaches to Investigate the Neonatal Gut Microbiome – Zakia Boudar – Frontiers in Pediatrics

Editorial: Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes – Arwyn Edwards – Microbiology

A Bayesian method for identifying associations between response variables and bacterial community composition – Adrian Verster – PLoS Computational Biology

GenBank as a Source to Monitor and Analyze Host-Microbiome Data – Vivek Ramanan – Bioinformatics

Phylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies – Hayley B Hassler – Microbiome

July 2, 2022

Have a nice weekend!

Highlights!

Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides – Miriam N. Ojima – The ISME Journalthis paper contributes to the understanding of the configuration of different bifidobacteria in response to human milk oligosaccharides. 

Genomes of six viruses that infect Asgard archaea from deep-sea sediments – Ian M. Rambo – Nature MicrobiologyBy using metagenomics, authors describe six relatively large viral genomes, capable to infect members of the Asgard superphylum. The paper remarks on the strange features found in those viral genomes.

TLR4 regulates RORγt+ regulatory T-cell responses and susceptibility to colon inflammation through interaction with Akkermansia muciniphila – Yaojiang Liu – MicrobiomeThis article demonstrates the existence of “a novel protective role of TLR4 against intestinal inflammation, wherein it can modulate A. muciniphila-associated immune responses”. 

Human and General Microbiome

Review: The microbiome and gut homeostasis – Jee-Yon Lee – Science 

Review: The role of microbiome: a novel insight into urolithiasis – Sen-Yuan Hong – Critical Reviews in Microbiology

Review: Symbiosis: the other cells in development – Tyler J Carrier – Development 

Dysbiosis of the Gut Microbiome Is Associated With Histopathology of Lung Cancer – Xiong Qin – Frontiers in Microbiology

Beneficial Microbes and Compounds

Perspective: Leveraging the Gut Microbiota to Predict Personalized Responses to Dietary, Prebiotic, and Probiotic Interventions – Sean M Gibbons – Advances in Nutrition

Akkermansia muciniphila Alters Gut Microbiota and Immune System to Improve Cardiovascular Diseases in Murine Model – Xin He – Frontiers in Microbiology

Impact of probiotics use on clinical outcomes of immune checkpoint inhibitors therapy in cancer patients – Luying Wan – Cancer Medicine

Review: The gut microbiome as possible mediator of the beneficial effects of very low calorie ketogenic diet on type 2 diabetes and obesity: a narrative review – G Defeudis – Eating and Weight Disorders

Animal Microbiome

The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction – Weiquan Wang – Nature Ecology & Evolution

Milk microbiomes of three great ape species vary among host species and over time – Sally L Bornbusch – Scientific Reports

Plant Microbiome

Fungal microbiome shifts on avocado fruit associated with a combination of postharvest chemical and physical interventions – Malick Bill – Journal of Applied Microbiology

Environmental Microbiome

Review: Priorities for ocean microbiome research – the Tara Ocean Foundation – Nature Microbiology

Microbiome Analysis Techniques and Tools

Protocol for correlation analysis of the murine gut microbiome and meta-metabolome using 16S rDNA sequencing and UPLC-MS – Xiaoqing Li – STAR Protocols

microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization – Yang Cao – Bioinformatics

June 29, 2022

General microbiome

Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station – Urbaniak et al. – Microbiome

Engineering the human gut commensal Bacteroides thetaiotaomicron with synthetic biology – Lai, Hayashi & Lu – Current Opinion in Chemical Biology

Factors shaping the abundance and diversity of the gut archaeome across the animal kingdom – Thomas et al. – Nature Communications

Human oral microbiome

Increase in Bifidobacterium is a characteristic of the difference in the salivary microbiota of pregnant and non-pregnant women – Kato et al. – BMC Oral Health

Human urinary microbiome

Concordance of Urinary Microbiota Detected by 16S rRNA Amplicon Sequencing Versus Expanded Quantitative Urine Culture – Vaughan et al. – American Journal of Obstetrics and Gynecology

Human gut microbiome

Dietary variety relates to gut microbiota diversity and abundance in humans – Huang et al. – European Journal of Nutrition

The gut microbiota composition in patients with right- and left-sided colorectal cancer and after curative colectomy, as analyzed by 16S rRNA gene amplicon sequencing – Suga et al. – BMC Gastroenterology

Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis – Troci et al. – Molecular Nutrition & Food Research

Functional changes of the gastric bypass microbiota reactivate thermogenic adipose tissue and systemic glucose control via intestinal FXR-TGR5 crosstalk in diet-induced obesity – Münzker et al. – Microbiome

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Perinatal transmission of a probiotic Bifidobacterium strain protects against early life stress-induced mood and gastrointestinal motility disorders – Zhu et al. – Food & Function

Leveraging Existing 16SrRNA Microbial Data to Define a Composite Biomarker for Autism Spectrum Disorder – Xu et al. – Microbiology Spectrum

Animal microbiome (for animals in the wild)

Gut microbiome of century-old snail specimens stable across time in preservation – Chalifour, Elder & Li – Microbiome

Plant, root, and soil microbiome

Soil-derived bacteria endow Camellia weevil with more ability to resist plant chemical defense – Zhang et al. – Microbiome

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

A genome and gene catalog of glacier microbiomes – Liu et al. – Nature Biotechnology

Bioinformatics / Data

Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans – Lemos et al. – Scientific Data

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota – Campos et al. – Poultry Science

[PREPRINT]Predicting metabolomic profiles from microbial composition through neural ordinary differential equations – Wang et al. – bioRxiv