May 29, 2023


Particular genomic and virulence traits associated with preterm infant-derived toxigenic Clostridium perfringens strains – Raymond Kiu – Nature Microbiology

Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach – Conor Feehily – Nature Communications

Human and General Microbiome

Expanding the repertoire of counterselection markers for markerless gene deletion in the human gut bacterium Phocaeicola vulgatus – André Neff – Anaerobe

Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection – Zheng Wang – Microbiome

Symbiotic microbiome Staphylococcus epidermidis restricts IL-33 production in allergic nasal epithelium via limiting the cellular necroptosis – Yung Jin Jeon – BMC Microbiology

Gut microbiome associated with low anterior resection syndrome after rectal cancer surgery – Min Jung Kim – Scientific Reports

Metabolomics Reveals Gut Microbiota Contribute to PPARα Deficiency-Induced Alcoholic Liver Injury – Ting Zhang – Journal of Proteome Research

Following your gut: the emerging role of the gut microbiota in predicting and treating immune-related adverse events – Antoine Desilets – Current Opinion in Oncology

Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma – Spyridon Megremis – Scientific Reports

The causal links between gut microbiota and COVID-19: A Mendelian randomization study – Jukun Song – Journal of Medical Virology

The Sexome – A proof of concept study into microbial transfer between heterosexual couples after sexual intercourse – Ruby Dixon – Forensic Science International

A systematic review of the protein composition of whole saliva in subjects with healthy periodontium compared with chronic periodontitis – Ana G Sánchez-Medrano – PloS ONE

Microbiome, Food and Diet

Metagenomic analysis and antibacterial activity of kefir microorganisms – Brianda D González-Orozco – Journal of Food Science

Fecal Metabolites as Biomarkers for Predicting Food Intake by Healthy Adults – Leila M Shinn – The Journal of Nutrition

More Microbes

Taxonogenomics of Culturomica massiliensis gen. nov., sp. nov., and Emergencia timonensis gen. nov., sp. nov. new bacteria isolated from human stool microbiota – Afaf Hamame – Scientific Reports

Animal Microbiome

Gut microbiome signatures of extreme environment adaption in Tibetan pig – Fangfang Zhao – NPJ Biofilms and Microbiomes

Holobiont Evolution: Population Theory for the Hologenome – Joan Roughgarden – The American Naturalist

Plant Microbiome

Integration of Phenotypes in Microbiome Networks for Designing Synthetic Communities: a Study of Mycobiomes in the Grafted Tomato System – Ravin Poudel – Applied and Environmental Microbiology

Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum – Jilu Che – Microbiology Spectrum

Bioinformatics, Microbiome Analysis and Techniques

MDM-Pred: a freely available web application for predicting the metabolism of drug-like compounds by the gut microbiota – A S Kolodnitsky – SAR and QSAR in Environmental Research

HONMF: integration analysis of multi-omics microbiome data via matrix factorization and hypergraph – Yuanyuan Ma – Bioinformatics 

Bayesian compositional regression with microbiome features via variational inference – Darren A V Scott – BMC Bioinformatics

The Pathfinder plasmid toolkit for genetically engineering newly isolated bacteria enables the study of Drosophila-colonizing Orbaceae – Katherine M Elston – ISME Communications

Review: Unravelling animal-microbiota evolution on a chip – Ostaizka Aizpurua – Trends in Microbiology

May 22, 2023

Have a nice day. Today we have a long list!


Airway dysbiosis accelerates lung function decline in chronic obstructive pulmonary disease – Weijie Liang – Cell Host & Microbe

An integrated tumor, immune and microbiome atlas of colon cancer – Jessica Roelands – Nature Medicine

General and Human Microbiome 

Skin microbiome alterations in upper extremity secondary lymphedema – Adana-Christine Campbell – PloS One

Isolation and identification of hyaluronan-degrading bacteria from Japanese fecal microbiota – Hazuki Akazawa – PloS One

Bacterial and metabolic phenotypes associated with inadequate response to ursodeoxycholic acid treatment in primary biliary cholangitis – Laura Martinez-Gili – Gut Microbes

Gut microbiota and its relation to inflammation in patients with bipolar depression: a cross-sectional study – Tingting Huang – Annals of General Psychiatry

Alterations in the Gut Microbiome and Metabolisms in Pregnancies with Fetal Growth Restriction – Zixin Tao – Microbiology Spectrum

16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients – Maartje Kristensen – Microbiology Spectrum

Single-Molecule Approach to 16S rRNA for Vaginal Microbiome Signatures in Response to Metronidazole Treatment – Hanyu Qin – Microbiology Spectrum

The presence of intratumoral Porphyromonas gingivalis correlates with a previously defined pancreatic adenocarcinoma, immune cell expression phenotype and with tumor resident, adaptive immune receptor features – Jacob C Kinskey – Carcinogenesis

Commentary: Microbiome is the key to preventing anastomotic leak in colorectal surgery – James M Kinross – Gut

Commentary: The aerobiome-health axis: a paradigm shift in bioaerosol thinking – Jake M Robinson – Trends in Microbiology

Review: Impact of the host microbiota on fungal infections: new possibilities for intervention? – Eve W L Chow – Advanced Drug Delivery Reviews

Review: Malnourished Microbes: Host-Microbiome Interactions in Child Undernutrition – Helen J Jones – Annual Review of Nutrition

Review: A narrative review from gut to lungs: non-small cell lung cancer and the gastrointestinal microbiome – Hely Shah – Translational Lung Cancer Research

Review: The interplay between oral microbiota, gut microbiota and systematic diseases – Xiujun Tan – Journal of Oral Microbiology

Animal Model Microbiome

Exposing new taxonomic variation with inflammation – a murine model-specific genome database for gut microbiome researchers – Ikaia Leleiwi – Microbiome

Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic – Huan Li – BMC Microbiology

Alterations of the gut microbiome and metabolic profile in CVB3-induced mice acute viral myocarditis – Qing Kong – BMC Microbiology

Seaweed polysaccharides treatment alleviates injury of inflammatory responses and gut barrier in LPS-induced mice – Yuanyuan He – Microbial Pathogenesis

Non-model Animal Microbiome

An entomopathogenic fungus exploits its host humoral antibacterial immunity to minimize bacterial competition in the hemolymph – Jia-Lin Wang – Microbiome

Engineered symbiotic bacteria interfering Nosema redox system inhibit microsporidia parasitism in honeybees – Haoyu Lang – Nature Communications

New insights into microbial and metabolite signatures of coral bleaching – Hao Sun – The Science of the Total Environment

Feeding hempseed cake alters the bovine gut, respiratory and reproductive microbiota – Thomas M Winders – Scientific Reports

Composition of mucus- and digesta-associated bacteria in growing pigs with and without diarrhea differed according to the presence of colonic inflammation – Farhad M Panah – BMC Microbiology

The microbiome and gene expression of honey bee workers are affected by a diet containing pollen substitutes – J Elijah Powell – PloS One

Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens – Xiang-Yu Wang – BMC Microbiology

Built Environment

Diversity and compositional differences of the airborne microbiome in a biophilic indoor environment – Akinobu Toyoda – Scientific Reports

Plant Microbiome

Review: Engineering the Crop Microbiota Through Host Genetics – Carmen Escudero-Martinez – Annual Review of Phytopathology

Root microbiome diversity and structure of the Sonoran desert buffelgrass (Pennisetum ciliare L.) – Angélica Jara-Servin – PloS One

Microbiome Analysis

News: Long-read sequencing for the metagenomic analysis of microbiomes – Tristan Free – BioTechniques

May 16, 2023

Happy Tuesday! Today’s microbiome digest is microbial ecology heavy, with articles focused on the gut microbiome, Antarctic endoliths’, water microbiomes, and more.

Human gut microbiome

Pathobionts in the tumour microbiota predict survival following resection for colorectal cancer – Alexander et al. – Microbiome

Gut microbiome transitions across generations in different ethnicities in an urban setting—the HELIUS study – van der Vossen et al. – Microbiome

Water and extremophile microbiome

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability – Ettinger et al. – Microbiome

Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes – Vigneron et al. – Microbiome

preprint: Allochthonous groundwater microorganisms affect coastal seawater microbial abundance, activity and diversity – Yanuka-Golub et al. – bioRxiv

Built environment

preprint: Microbial Diversity on Ancestral Halls with Different Visitor Flow Rates Using Amplicon Sequencing – Liu et al. – bioRxiv


Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies – Orellana et al. – Microbiome

May 15, 2023

Human Microbiome

Assessing the relationship between gut microbiota and irritable bowel syndrome: a two-sample Mendelian randomization analysis – Bin Liu – BMC Gastroenterology

The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis – A C Anderson – Annals of Clinical Microbiology and Antimicrobials

New evidence for the role of gut microbiota on atrial fibrillation development – Christopher Papandreou – EBioMedicine

Influence of grape consumption on the human microbiome – Asim Dave – Scientific Reports

Microbiota transplant to control inflammation in a patient with NLRC4 gain-of-function-induced disease – Claudia Bracaglia – The Journal of Allergy and Clinical Immunology

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Animal Microbiome

Integrated microbiome-metabolome-genome axis data of Laiwu and Lulai pigs – Xueshuang Lai – Scientific data

Positive associations matter: Microbial relationships drive tick microbiome composition – Nicholas M Fountain-Jones – Molecular Ecology

In Vitro Ileal Fermentation is Affected More by the Fiber Source Fermented than the Ileal Microbial Composition in Growing Pigs – Anna Me Hoogeveen – Current Developments in Nutrition

Oroxin B improves metabolic-associated fatty liver disease by alleviating gut microbiota dysbiosis in a high-fat diet-induced rat model – Yuhong Huang – European Journal of Pharmacology

Plant Microbiome

Drought stress mediated differences in phyllosphere microbiome and associated pathogen resistance between male and female poplars – Tiantian Lin – The Plant Journal 

Environmental Microbiome

Looking into sewage: how far can metagenomics help to detect human enteric viruses? – Julien Schaeffer – Frontiers in Microbiology

Metagenomic insights into the potential risks of representative bio/non-degradable plastic and non-plastic debris in the upper and lower reaches of Haihe Estuary, China – Xinhai Zhao – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

A Bayesian joint model for compositional mediation effect selection in microbiome data – Jingyan Fu – Statistics in Medicine

May 12, 2023

Today’s digest features studies on human respiratory tract, mouse models, bovine milk microbiome, and more. See you at #MVIF next week!

Respiratory tract microbiome

Review: Ecology of the respiratory tract microbiome – Ana Elena Pérez-Cobas – Trends in Microbiology

Cervicovaginal microbiome

The cervical microbiota of Hispanics living in Puerto Rico is highly volatile and dominated by Lactobacillus iners regardless of HPV status – Daniela Vargas-Robles – bioRxiv

Gut microbiome

Key determinants of success in fecal microbiota transplantation: From microbiome to clinic – Serena Porcari – Cell Host & Microbes

Profiling the human intestinal environment under physiological conditions – Dari Shalon – Nature

Interaction between gut microbiota and sex hormones and their relation to sexual dimorphism in metabolic diseases – Jose Antonio Santos-Marcos – Biology of Sex Differences

Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis – Paige Salerno – bioRxiv

Animal microbiome

Metagenomic analysis of milk microbiota in the bovine subclinical mastitis – Giulia Alessandri – bioRxiv

Animal experiments

MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice – Paolo Manghi – Cell Reports


ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning – Olga Mineeva – Plos Computational Biology


Catch me if you can: capturing microbial community transformation by extracellular DNA using Hi-C sequencing – David Calderón-Franco – Antonie van Leeuwenhoek

Built environment

The microbiome of an outpatient rehabilitation clinic and predictors of contamination: A pilot study – Gabriella Brigando – PlosOne

May 8, 2023

General and Human Microbiome

Microbial β-glucuronidases drive human periodontal disease etiology – Adam D Lietzan – Science Advances

Vaginal epithelial dysfunction is mediated by the microbiome, metabolome, and mTOR signaling – Alicia R Berard – Cell Reports

Causal relationship between Gut Microbiota and Obstructive sleep apnea – Yi Wei – Archives of Gerontology and Geriatrics

Changes in the intestinal microbiota of children with hand, foot, and mouth disease under 3 years old – Su Yue Zhu – Medicine

Reduced microbial diversity of the nasopharyngeal microbiome in household contacts with latent tuberculosis infection – Cinthya Ruiz-Tagle – Scientific Reports

Pitfalls in sampling and analyzing low-biomass human nasal microbiome samples – Petra Pjevac – The Journal of Allergy and Clinical Immunology

The saga of non-traditional risk factors continues with proteomics, microbiome, ozone, ketone bodies, and depression: let us rethink prevention – Filippo Crea – European Heart Journal

Review: Stress, inflammation, microbiome and depression – Eva M Medina-Rodriguez – Pharmacology, Biochemistry, and Behavior

Review: Fungi and cancer – Aurelia Saftien – Gut

Review: L-Fucose is involved in human-gut microbiome interactions – Jungyeon Kim – Applied Microbiology and Biotechnology

Beneficial Microbes, Compounds and Interventions

Vitamin K2 supplementation improves impaired glycemic homeostasis and insulin sensitivity for type 2 diabetes through gut microbiome and fecal metabolites – Yuntao Zhang – BMC Medicine

Intermittent fasting alleviates non-alcoholic steatohepatitis by regulating bile acid metabolism and promoting fecal bile acid excretion in high-fat and high-cholesterol diet fed mice – Xiaozhuan Lin – Molecular Nutrition & Food Research

Animal Microbiome

Gut microbiome of mealworms (Tenebrio molitor Larvae) show similar responses to polystyrene and corn straw diets – Tursunay Mamtimin – Microbiome

Plant Microbiome

Review: The good, the bad, and the phosphate: regulation of beneficial and detrimental plant-microbe interactions by the plant phosphate status – Michael Paries – The New Phytologist

May 5, 2023

Today’s microbiome digest is a grab bag that includes ten simple rules for working with other people’s code, an article examining Wolbachia infections in native cockroach populations, and an article examining the role in lactic acid in shaping the human microbiome. Also highlighted is an article focused on human viruses residing within our cells and tissues, which demonstrated a unique virome in nine different human organs through targeted-enrichment viral metagenomics and virus specific qPCRs.

Happy reading!

General microbiome

The structure of prevacuolar compartments in Neurospora crassa as observed with super-resolution microscopy – Bowman – PLOS One

Phylogenetic trees of closely related bacterial species and subspecies based on frequencies of short nucleotide sequences – Nakano et al. – PLOS One

***Unmasking the tissue-resident eukaryotic DNA virome in humans – Pyöriä et al. – Nucleic Acids Research

Predicting partner fitness based on spatial structuring in a light-driven microbial community – Sakkos et al. – PLOS Computational Biology

Multi-site human microbiome

Evaluation of alcohol-free mouthwash for studies of the oral microbiome – Yano et al. – PLOS One

A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome – Zhang et al. – Microbiome

Human gut microbiome

Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the “Lunar Palace 365” experiment – Hao et al. – Microbiome

Animal microbiome

Wolbachia infection in native populations of Blattella germanica and Periplaneta americana – Choubdar et al. – PLOS One

Plant, root, and soil microbiome

Bacterial and fungal community composition and community-level physiological profiles in forest soils – Kunito et al. – PLOS One

Water and extremophile microbiome

Predicting microbial community compositions in wastewater treatment plants using artificial neural networks – Liu et al. – Microbiome

Open ocean and coastal strains of the N2-fixing cyanobacterium UCYN-A have distinct transcriptomes – Muñoz-Marín et al. – PLOS One

Meta-organism gene expression reveals that the impact of nitrate enrichment on coral larvae is mediated by their associated Symbiodiniaceae and prokaryotic assemblages – Tong et al. – Microbiome


Ten simple rules for working with other people’s code – Pilgrim et al. – PLOS Computational Biology

Predicting microbe organisms using data of living micro forms of life and hybrid microbes classifier – Raza et al. – PLOS One

iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria – Roux et al. – PLOS Biology

May 1, 2023

Human and General Microbiome

Th17 cells sense microbiome to promote depressive-like behaviors – Eva M Medina-Rodriguez – Microbiome

Obese-associated gut microbes and derived phenolic metabolite as mediators of excessive motivation for food reward – Alice de Wouters d’Oplinter – Microbiome

Alteration of taste perception, food neophobia and oral microbiota composition in children with food allergy – Enza D’Auria – Scientific Reports

Translocating Lactobacillus torments tumors via tryptophan catabolism – Márcia S Pereira – Cell

Global trends in research related to the links between microbiota and antibiotics: a visualization study – Sa’ed H Zyoud – Scientific Reports

Modulation of antibiotic effects on microbial communities by resource competition – Daniel P Newton – Nature Communications

Review: Less is more: Antibiotics at the beginning of life – Martin Stocker – Nature Communications

Review: The interaction between autophagy, Helicobacter pylori, and gut microbiota in gastric carcinogenesis – Ali Nabavi-Rad – Trends in Microbiology

Review: The orchestra of human bacteriome by hormones – Arif Luqman – Microbial Pathogenesis

Review: Targeting the human gut microbiome with small-molecule inhibitors – Amelia Y M Woo – Nature Reviews. Chemistry

Review: A precision environmental health approach to prevention of human disease – Andrea Baccarelli – Nature Communications

Review: Emerging role of bacterial outer membrane vesicle in gastrointestinal tract – Cheng-Mei Tian – Gut Pathogens

Review: The Gut Microbiota – Brain Axis: Potential Mechanism of Drug Addiction – Xiao Luo – Current Topics in Medicinal Chemistry

Beneficial Microbes and Compounds

The effects of live and pasteurized Akkermansia muciniphila on DSS-induced ulcerative colitis, gut microbiota, and metabolomics in mice – Liangyu Xue – Food & Function

Inulin diet uncovers complex diet-microbiota-immune cell interactions remodeling the gut epithelium – Renan Oliveira Corrêa – Microbiome

Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice – Haibo Tang – Life Sciences

Animal Microbiome

Intestinal epigenotype of Atlantic salmon (Salmo salar) associates with tenacibaculosis and gut microbiota composition – Søren B Hansen – Genomics

Review: Environmental Effects on Bee Microbiota – Phuong N Nguyen – Microbial Ecology

Review: Illuminating the Oral Microbiome and its Host Interactions: Animal models of disease – George Hajishengallis – FEMS Microbiology Reviews

Plant Microbiome

Review: How does plant sex alter microbiota assembly in dioecious plants? – Qingxue Guo – Trends in Microbiology

Environmental Microbiome

Compositional Changes in Sediment Microbiota Are Associated with Seasonal Variation of the Water Column in High-Altitude Hyperarid Andean Lake Systems – Ignacio Ramos-Tapia – Microbiology Spectrum

Built Environment

Dynamics of microbial community composition during degradation of silks in burial environment – Bowen Wang – The Science of the Total Environment


DeepMicroGen: a generative adversarial network based method for longitudinal microbiome data imputation – Joung Min Choi – Bioinformatics

April 26, 2023

General microbiome

[PREPRINT]Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Klümper et al. – bioRxiv

Pregnancy and early life

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes – Graspeuntner et al. – Microbiology Spectrum

Human gut microbiome

Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer – Oosterlinck et al. – Microbiome

[REVIEW]Fecal microbiota transplantation for recurrent C. difficile infection in patients with inflammatory bowel disease: A systematic review and meta-analysis – Porcari et al. – Journal of Autoimmunity

[REVIEW]Alcohol, the gut microbiome, and liver disease – Jew & Hsu – JGH

[REVIEW]Microbial metabolites in colorectal tumorigenesis and cancer therapy – Liu et al. – Gut Microbes

Human biliary microbiome

Neoadjuvant therapy does not impact the biliary microbiome in patients with pancreatic cancer – Behrens et al. – Journal of Surgical Oncology

Animal microbiome (for animals in the wild)

Indirect maternal effects via nest microbiome composition drive gut colonization in altricial chicks – Diez-Mendez et al. – Molecular Ecology

The gut microbiome of solitary bees is mainly affected by pathogen assemblage and partially by land use – de Landa et al. – Environmental Microbiome

Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin – Masasa et al. – Microbiology Spectrum

The microbiota in feces of domestic pigeons in Seoul, Korea – Oh et al. – Heliyon

Plant, root, and soil microbiome

Characterization of the Rhizosphere Bacterial Microbiome and Coffee Bean Fermentation in the Castillo-Tambo and Bourbon Varieties in the Popayán-Colombia Plateau – Solis Pino et al. – BMC Plant Biology

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

Hydrochemical and Seasonally Conditioned Changes of Microbial Communities in the Tufa-Forming Freshwater Network Ecosystem – Cackovic et al. – mSphere


[PREPRINT]ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization – Yang et al. – arXiv

April 24, 2023

Human and General Microbiome

Review: Effects of ultra-processed foods on the microbiota-gut-brain axis: The bread-and-butter issue – Zheyi Song – Food Research International 

Review: The emerging role of the small intestinal microbiota in human health and disease – Renate Ruigrok – Gut Microbes

Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma – Takuma Sasaki – Esophagus

Multi-omics signatures in new-onset diabetes predict metabolic response to dietary inulin: findings from an observational study followed by an interventional trial – N Ďásková – Nutrition & Diabetes

Comparison of Conjunctival Sac Microbiome between Low and High Myopic Eyes – Kang Xiao – Journal of Microbiology

Sentinel or accomplice – gut microbiota and microglia cross-talk in disorders of gut-brain interaction – Haonan Zheng – Protein & Cell

Beneficial Microbes and Compounds

Effects of dietary fibers or probiotics on functional constipation symptoms and roles of gut microbiota: a double-blinded randomized placebo trial – Hao Lai – Gut Microbes

Review: Use of probiotic lactobacilli in the treatment of vaginal infections: In vitro and in vivo investigations – Peng Liu – Frontiers in Cellular and Infection Microbiology

Animal Microbiome

The hindgut microbiome contributes to host oxidative stress in postpartum dairy cows by affecting glutathione synthesis process – Fengfei Gu – Microbiome

Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons – Qi Li – NPJ Biofilms and Microbiomes

Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community – Manar El Samak – Marine Genomics

Vibrio cholerae Invasion Dynamics of the Chironomid Host Are Strongly Influenced by Aquatic Cell Density and Can Vary by Strain – Dianshu Zhao – Microbiology Spectrum

Antibiotic Conditioning Shapes Pseudosterile Mouse Models by Deleting Colonic Microbes Rather than Small Intestinal Microbes – Qingxue Chen – Microbiology Spectrum

Plant Microbiome

Microbiota-mediated nitrogen fixation and microhabitat homeostasis in aerial root-mucilage – Zhiqiang Pang – Microbiome

Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions – Simrandeep Singh – Environmental Microbiome

Effects of vermicompost leachate on nitrogen, phosphorus, and microbiome in a food waste bioponic system – Sumeth Wongkiew – Journal of Environmental Management

The effect of wheat genotype on the microbiome is more evident in roots and varies through time – Liliana Quiza – ISME Communications

Environmental Microbiome

Disentangling temporal associations in marine microbial networks – Ina Maria Deutschmann – Microbiome

Evaluating the Reproducibility of Amplicon Sequencing Data Derived from Deep-Sea Cold Seep Sediment-Associated Microbiota – Jie Kong – Microbiology Spectrum

Built Environment

BioMateriOME: to understand microbe-material interactions within sustainable, living architectures – Beatriz Delgado Corrales – Advances in Applied Microbiology

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Deciphering associations between gut microbiota and clinical factors using microbial modules – Ran Wang – Bioinformatics

SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis – Jackie Zorz – ISME Communications

Integrating Multi-Omics Data to Construct Reliable Interconnected Models of Signaling, Gene Regulatory, and Metabolic Pathways – Krishna Kumar – Methods in Molecular Biology


Interactions between the lipidome and genetic and environmental factors in autism – Chloe X Yap – Nature Medicine