Category Archives: General Microbiome

April 14, 2023

Posted on by

Today’s reading recommendation includes microbiome from sites with low anthropogenic impact, drinking water microbiome, and more.

If you have only a minute for reading then your must read is this amazing summary thread on how you should be careful with making assumptions ⬇️

See you at #MVIF next week!

Global resistome

Global trends in antimicrobial resistance on organic and conventional farms – Eldon Ager – bioRxiv

*Microbiome diversity: A barrier to the environmental spread of antimicrobial resistance? – Uli Klümper – bioRxiv

Mother-to-infant microbiome

Mother-to-infant microbiota transmission and infant microbiota development across multiple body sites – Debby Bogaert – Cell Host & Microbe

Human gut microbiome

The Local Tumor Microbiome Is Associated with Survival in Late-Stage Colorectal Cancer Patients – Justine W. Debelius – Microbiology Spectrum

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy – Ruben Ladeira, Julien Tap, Muriel Derrien – Microbiome Research Reports

Water microbiome

The microbial dark matter and “wanted list” in worldwide wastewater treatment plants – Yulin Zhang – Microbiome

*Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems – David Calderón-Franco – Water Research

Animal experiment

Probiotics of Lacticaseibacillus paracasei SD1 and Lacticaseibacillus rhamnosus SD11 attenuate inflammation and β-cell death in streptozotocin-induced type 1 diabetic mice – Jongdee Nopparat – PlosOne

Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem – Madeleine Spatz – Microbiome

*Experimental Factors Influence Diversity Metrics of the Gut Microbiome in Laboratory Mice – Rikeish R. Muralitharan – bioRxiv

Virome & phages

Expanding known viral diversity in the healthy infant gut – Shiraz A. Shah – Nature Microbiology

Large-scale phage cultivation for commensal human gut bacteria – Juntao Shen – Cell Host & Microbe

Methodology

Reducing bias in microbiome research: Comparing methods from sample collection to sequencing – Jolanda Kool – Frontiers in Microbiology

In Vitro Modelling of Oral Microbial Invasion in the Human Colon – Lucie Etienne-Mesmin – Microbiology Spectrum

Bioinformatics

Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes – Wojtek Bazant – Microbiome

April 10, 2023

Posted on by

Human and General Microbiome

Review: Exploring the Influence of Gut Microbiome on Energy Metabolism in Humans – Julia Montenegro – Advances in Nutrition

Review: Ruminococcus gnavus: friend or foe for human health – Emmanuelle H Crost – FEMS Microbiology Reviews

Uncovering the special microbiota associated with occurrence and progression of gastric cancer by using RNA-sequencing – Bin Ai – Scientific Reports

Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism – Xiangwei Hu – NPJ Biofilms and Microbiomes

The secondary bile acid isoursodeoxycholate correlates with post-prandial lipemia, inflammation, and appetite and changes post-bariatric surgery – Panayiotis Louca – Cell Reports. Medicine

Forging the microbiome to help us live long and prosper – Rachel R Rock – PLoS Biology

Meta-analysis reveals Helicobacter pylori mutual exclusivity and reproducible gastric microbiome alterations during gastric carcinoma progression – Yan Li – Gut Microbes

Beneficial Microbes and Compounds

Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites – Guangqi Gao – EBioMedicine

Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems – Samuel Zimmerman – mSystems

New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota – Akil Akhtar – Communications Biology

Animal Microbiome

Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community – Jacob Agerbo Rasmussen – Microbiological Research

Plant Microbiome

Cofunctioning of bacterial exometabolites drives root microbiota establishment – Felix Getzke – PNAS

Environmental Microbiome

Review: Unveiling the role of emerging metagenomics for the examination of hypersaline environments – Kiran Dindhoria – Biotechnology & Genetic Engineering Reviews

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Multi-scale Adaptive Differential Abundance Analysis in Microbial Compositional Data – Shulei Wang – Bioinformatics

The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection – Ruijie Xu – PloS ONE

An in vitro platform for study of the human gut microbiome under an oxygen gradient – James Comolli – Biomedical Microdevices

Machine learning model to predict obesity using gut metabolite and brain microstructure data – Vadim Osadchiy – Scientific Reports

April 3, 2023

Posted on by

Human and General Microbiome

Review: Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome – Stephen R Stockdale – Current Opinion in Microbiology

No evidence for a common blood microbiome based on a population study of 9,770 healthy humans – Cedric C S Tan – Nature Microbiology

Genetic correlations between Alzheimer’s disease and gut microbiome genera – Davis Cammann – Scientific Reports

Limitations of using 16S rRNA microbiome sequencing to predict oral squamous cell carcinoma – Christopher Delaney – APMIS

Mendelian randomization analyses reveal causal relationships between the human microbiome and longevity – Xiaomin Liu – Scientific Reports

Genomics of Invasive Cutibacterium acnes Isolates from Deep-Seated Infections – Anna Both – Microbiology Spectrum

Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition – Kayla A Carter – mSystems

Review: Interspecies Interactions within the Host: the Social Network of Group B Streptococcus – Marlyd E Mejia – Infection and Immunity

Beneficial Microbes and Compounds

Review: Kefir as a therapeutic agent in clinical research: a scoping review – Milena Klippel Bessa – Nutrition Research Reviews

Interaction between β-glucans and gut microbiota: a comprehensive review – Reza Karimi – Critical Reviews in Food Science and Nutrition

Combination of vitamin D and probiotics inhibits chemically induced colorectal carcinogenesis in Wistar rats – Carolina S de Oliveira – Life Sciences

Animal Microbiome

Review: Recent advancements in coral health, microbiome interactions and climate change – Nizam Ashraf – The Science of the Total Environment

Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome – Line Jensen Ostenfeld – PloS One

Microbial Species-Area Relationships on the Skins of Amphibian Hosts – Fan Yang – Microbiology Spectrum

Intestinal microbiota of Nearctic-Neotropical migratory birds vary more over seasons and years than between host species – Heather R Skeen – Molecular Ecology

Food Microbiome

A unique case in which Kimoto-style fermentation was completed with Leuconostoc as the dominant genus without transitioning to Lactobacillus – Kohei Ito – Journal of Bioscience and Bioengineering

Built Environment

Holobiont Urbanism: sampling urban beehives reveals cities’ metagenomes – Elizabeth Hénaff – Environmental Microbiome

Microbiome Analysis: Protocols, Resources, Tools and Techniques

Contamination detection and microbiome exploration with GRIMER – Vitor C Piro – GigaScience

Annotation-free discovery of functional groups in microbial communities – Xiaoyu Shan – Nature Ecology & Evolution

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis – Jinlong Ru – Gut Microbes

Sequence-Based Characterization of Microalgal Microbiomes: Impact of DNA Extraction Protocol on Yield and Community Composition – Line Roager – Microbiology Spectrum

Preprint: Identifying keystone species in microbial communities using deep learning – Xu-Wen Wang – bioRxiv

March 27, 2023

Posted on by

Human and General Microbiome

The genomic landscape of reference genomes of cultivated human gut bacteria – Xiaoqian Lin – Nature Communications

Inhibition of a Microbiota-derived Peptide Ameliorates Established Acute Lung Injury – Valeria Fridman D’Alessandro – The American Journal of Pathology

Eubiotic effect of rifaximin is associated with decreasing abdominal pain in symptomatic uncomplicated diverticular disease: results from an observational cohort study – Vladimir Ivashkin – BMC Gastroenterology

Mucin glycans drive oral microbial community composition and function – Chloe M Wu – NPJ Biofilms and Microbiomes

Changes in gut microbial community upon chronic kidney disease – Wu Liu – PloS One

A Pilot Study Exploring Temporal Development of Gut Microbiome/Metabolome in Breastfed Neonates during the First Week of Life – Imad Awan – Pediatric Gastroenterology, Hepatology & Nutrition

Realising respiratory microbiomic meta-analyses: time for a standardised framework – David Broderick – Microbiome

Vulvovaginal yeast infections during pregnancy and perinatal outcomes: systematic review and meta-analysis – Ranjana M S Gigi – BMC Women’s Health

Preprint: Hadza Prevotella Require Diet-derived Microbiota Accessible Carbohydrates to Persist in Mice – Rebecca H Gellman – bioRxiv

Review: Membrane lipids from gut microbiome-associated bacteria as structural and signalling molecules – Eileen Ryan – Microbiology

Review: Impact of Intermittent Fasting on the Gut Microbiota: A Systematic Review – Theodoro Pérez-Gerdel – Advanced Biology

Animal Microbiome

Wolbachia endosymbiotic bacteria alter the gut microbiome in the fly Drosophila nigrosparsa – Matsapume Detcharoen – Journal of Invertebrate Pathology

A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota – Ren Dodge – Nature Communications

Plant Microbiome

The core metabolome and root exudation dynamics of three phylogenetically distinct plant species – Sarah McLaughlin – Nature Communications

Co-occurrence network analysis unveils the actual differential impact on the olive root microbiota by two Verticillium wilt biocontrol rhizobacteria – Martina Cardoni – Environmental Microbiome

Environmental Microbiome

Investigating the eco-evolutionary response of microbiomes to environmental change – Jennifer B H Martiny – Ecology Letters

Microbiome Analysis: Resources, Tools and Techniques

In silico evaluation and selection of the best 16S rRNA gene primers for use in next-generation sequencing to detect oral bacteria and archaea – Alba Regueira-Iglesias – Microbiome

DeepGeni: deep generalized interpretable autoencoder elucidates gut microbiota for better cancer immunotherapy – Min Oh – Scientific Reports

Flex Meta-Storms elucidates the microbiome local beta-diversity under specific phenotypes – Mingqian Zhang – Bioinformatics

Preprint: Microbiome Preterm Birth DREAM Challenge: Crowdsourcing Machine Learning Approaches to Advance Preterm Birth Research – Jonathan L Golob – medRxiv

March 20, 2023

Posted on by

Human and General Microbiome

Bacteria require phase separation for fitness in the mammalian gut – Emilia Krypotou – Science

Is there a placental microbiota? A critical review and re-analysis of published placental microbiota datasets – Jonathan J Panzer – BMC Microbiology

Gut-microbiome-expressed 3β-hydroxysteroid dehydrogenase degrades estradiol and is linked to depression in premenopausal females – Di Li – Cell Metabolism

Metagenomic association analysis of cognitive impairment in community-dwelling older adults – Jincheng Li – Neurobiology of Disease

Fusobacterium nucleatum promotes esophageal cancer early occurrence through upregulation of IL-32/PRTN3 expression – Jing Lei – Cancer Science

Review: Postbiotics Implication in the Microbiota-Host Intestinal Epithelial Cells Mutualism – Harpreet Kaur – Probiotics and Antimicrobial Proteins

Review: Microbiota and growth among infants and children in low-income and middle-income settings – James M Njunge – Current Opinion in Clinical Nutrition and Metabolic Care

Review: Cardiometabolic health, diet and the gut microbiome: a meta-omics perspective – Mireia Valles-Colomer – Nature Medicine

Review: Oral polymicrobial communities: Assembly, function, and impact on diseases – George Hajishengallis – Cell Host & Microbe

Review: Gut microbiota: a non-target victim of pesticide-induced toxicity – Tusha Sharma – Gut Microbes

Perspective: Human microbiome research: Growing pains and future promises – Jens Puschhof – PLoS Biology

Beneficial Microbes and Compounds

Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis – Xinyue Wang – Science Advances

Lactobacillus rhamnosus GG cell-free supernatant as a novel anti-cancer adjuvant – Rossella Salemi – Journal of Translational Medicine

Environmental Microbiome

Community dynamics of microbial eukaryotes in intertidal mudflats in the hypertidal Bay of Fundy – Eke I Kalu – ISME Communications

Other Microbes

Biointerface mineralization generates ultraresistant gut microbes as oral biotherapeutics – Zhongmin Geng – Science Advances

Genomic diversity of non-diarrheagenic fecal Escherichia coli from children in sub-Saharan Africa and south Asia and their relatedness to diarrheagenic E. coli – Tracy H Hazen – Nature Communications

Microbiome Analysis: Tools and Techniques

Spatial profiling of microbial communities by sequential FISH with error-robust encoding – Zhaohui Cao – Nature Communications

sBGC-hm: An atlas of secondary metabolite biosynthetic gene clusters from the human gut microbiome – Huixi Zou – Bioinformatics

Protocol: Bioinformatic and Statistical Analysis of Microbiome Data – Youngchul Kim – Methods in Molecular Biology

Protocol: Multi-omics Data Deconvolution and Integration: New Methods, Insights, and Translational Implications – Xuefeng Wang – Methods in Molecular Biology

March 13, 2023

Posted on by

Human and General Microbiome

Dysbiosis of a microbiota-immune metasystem in critical illness is associated with nosocomial infections – Jared Schlechte – Nature Medicine

Altered infective competence of the human gut microbiome in COVID-19 – Laura de Nies – Microbiome

Impact of high altitude on composition and functional profiling of oral microbiome in Indian male population – Manisha Kumari – Scientific Reports

Incidence of Breast Cancer and Enterococcus Infection: A Retrospective Analysis – Matthew Cardeiro – World Journal of Oncology

Multi-omics studies in interpreting the evolving standard model for immune functions – Dipyaman Ganguly – Briefings in Functional Genomics

Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans – Jinuk Jeong – Journal of oral Microbiology

A transcriptomic insight into the human sperm microbiome through next-generation sequencing – Celia Corral-Vazquez – Systems Biology in Reproductive Medicine

Beneficial Microbes and Compounds

Metformin alleviates liver fibrosis in mice by enriching Lactobacillus sp. MF-1 in the gut microbiota – Tao Yang – Biochimica et Biophysica Acta

Animal Microbiome

Microbiota alters the metabolome in an age- and sex- dependent manner in mice – Kirsty Brown – Nature Communications

IL-22 alters gut microbiota composition and function to increase aryl hydrocarbon receptor activity in mice and humans – Jordan S Mar – Microbiome

Decreased Paneth cell α-defensins promote fibrosis in a choline-deficient L-amino acid-defined high-fat diet-induced mouse model of nonalcoholic steatohepatitis via disrupting intestinal microbiota – Shunta Nakamura – Scientific Reports

Plant Microbiome

Microbiota and functional analyses of nitrogen-fixing bacteria in root-knot nematode parasitism of plants – Ye Li – Microbiome

Non-volatile metabolites mediating plant interactions with insect herbivores – Mei Luo – The Plant Journal

Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress – Bo Wang – Frontiers in Microbiology

Review: Emerging Pathways for Engineering the Rhizosphere Microbiome for Optimal Plant Health – Shengdie Yang – Journal of Agricultural and food Chemistry

Microbiome Analysis: Tools and Techniques

A bayesian zero-inflated dirichlet-multinomial regression model for multivariate compositional count data – Matthew D Koslovsky – Biometrics

Determining the most accurate 16S rRNA hypervariable region for taxonomic identification from respiratory samples – Ruben López-Aladid – Scientific Reports

March 9, 2023

Posted on by

Today’s digest features studies on latent and established antibiotic resistance genes in microbiomes, newborn skin microbiome, drinking water microbiome after COVID-19 pandemic, and more. Listen to the science behind The Last of Us!

See you at #MVIF next week!

Antibiotic resistome

*Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes – Juan Salvador Inda-Díaz – Microbiome

Human skin

*The skin microbiome in the first year of life and its association with atopic dermatitis – Alexis Rapin – Allergy

Urinary tract

Review: Microbiome in urological diseases: Axis crosstalk and bladder disorders – Hae Woong Choi – Investigative and Clinical Urology

Human gut

Human microbiome variance is underestimated – Fergus Shanahan – Current Opinion in Microbiology

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

Microbial community-scale metabolic modeling predicts personalized short-chain-fatty-acid production profiles in the human gut – Nick Bohmann – bioRxiv

Review: Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics – Aleksandr A. Arzamasov & Andrei L. Osterman – Critical Reviews in Biochemistry and Molecular Biology

Guts Imbalance Imbalances the Brain: A Review of Gut Microbiota Association With Neurological and Psychiatric Disorders – Laura Mitrea – Frontiers in Medicine

Drinking water

*Gradual Recovery of Building Plumbing-Associated Microbial Communities after Extended Periods of Altered Water Demand during the COVID-19 Pandemic – Solize Vosloo – Environmental Science & Technology

March 6, 2023

Posted on by

Human and General Microbiome

Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection – Jiarui Li – Microbiome

Population-level impacts of antibiotic usage on the human gut microbiome – Kihyun Lee – Nature Communications

A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem – Toshihiko Katoh – Nature Chemical Biology

Microbiota-derived genotoxin tilimycin generates colonic stem cell mutations – Lisa Pöltl – Cell Reports

Review: Impact of caloric restriction on the gut microbiota – Lara Kern – Current Opinion in Microbiology

Animal Microbiome

Romboutsia lituseburensis JCM1404 supplementation ameliorated endothelial function via gut microbiota modulation and lipid metabolisms alterations in obese rats – Honggang Yin – FEMS Microbiology Letters

Disparate population and holobiont structure of pocilloporid corals across the Red Sea gradient demonstrate species-specific evolutionary trajectories – Carol Buitrago-López – Molecular Ecology

Omics and imaging combinatorial approach reveals butyrate-induced inflammatory effects in the zebrafish gut – Adrià López Nadal – Animal Microbiome

Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis – Fengfei Gu – Microbiome

Maternal effects drive intestinal development beginning in the embryonic period on the basis of maternal immune and microbial transfer in chickens – Haizhou Gong – Microbiome

Mouse mammary tumor virus is implicated in severity of colitis and dysbiosis in the IL-10(-/-) mouse model of inflammatory bowel disease – Heather Armstrong – Microbiome

Microplastics affect arsenic bioavailability by altering gut microbiota and metabolites in a mouse model – Shan Chen – Environmental Pollution 

Substantial viral and bacterial diversity at the bat-tick interface – Ayda Susana Ortiz-Baez – Microbial Genomics

Review: Perturbation of maternal gut microbiota in mice during a critical perinatal window influences early neurobehavioral outcomes in offspring – Cassandre Morel – Neuropharmacology

Plant and Soil Microbiome

Local environment drives rapid shifts in composition and phylogenetic clustering of seagrass microbiomes – Melissa R Kardish – Scientific Reports

Experimental community coalescence sheds light on microbial interactions in soil and restores impaired functions – Sarah Huet – Microbiome

Microbiome Analysis: Tools and Techniques

Infants’ gut microbiome data: A Bayesian Marginal Zero-inflated Negative Binomial regression model for multivariate analyses of count data – Morteza Hajihosseini – Computational and Structural Biotechnology Journal

From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools – Robyn J Wright – Microbial Genomics

Using strain-resolved analysis to identify contamination in metagenomics data – Yue Clare Lou – Microbiome

Preprint: Transkingdom Network Analysis (TkNA): a systems approach inferring causal factors underlying host-microbiota interactions – Nolan K Newman – bioRxiv

February 27, 2023

Posted on by

Highlights!

Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4 – Aitor Blanco-Míguez – Nature Biotechnology

Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease – Raaj S Mehta – Nature Medicine

Human and General Microbiome

Interpersonal variability of the human gut virome confounds disease signal detection in IBD – Stephen R Stockdale – Communications Biology

Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients – Zhi Ao – BMJ Open Respiratory Research

Comparing the gut microbiome of obese, African American, older adults with and without mild cognitive impairment – Andrew McLeod – PloS One

Beneficial Microbes and Compounds

Capacity of a Microbial Synbiotic To Rescue the In Vitro Metabolic Activity of the Gut Microbiome following Perturbation with Alcohol or Antibiotics – Braden T Tierney – Applied and Environmental Microbiology

Animal Microbiome

A microbiota and dietary metabolite integrates DNA repair and cell death to regulate embryo viability and aneuploidy during aging – Robert Sonowal – Science Advances

A longitudinal survey in the wild reveals major shifts in fish host microbiota after parasite infection – Eglantine Mathieu-Bégné – Molecular Ecology

Matrine alleviates depressive-like behaviors via modulating microbiota-gut-brain axis in CUMS-induced mice – Ming Zhang – Journal of Translational Medicine

Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers – Huasong Bai – Archives of Microbiology

Environmental Microbiome

Enzyme adaptation to habitat thermal legacy shapes the thermal plasticity of marine microbiomes – Ramona Marasco – Nature Communications

Microbiome Analysis: Tools and Techniques

Review: Computational methods and challenges in analyzing intratumoral microbiome data – Qi Wang – Trends in Microbiology

Robust Bioinformatics Approaches Result in the First Polygenic Risk Score for BMI in Greek Adults – Maria Kafyra – Journal of Personalized Medicine

Development of a tongue image-based machine learning tool for the diagnosis of gastric cancer: a prospective multicentre clinical cohort study – Li Yuan – EClinicalMedicine

Latent dirichlet allocation for double clustering (LDA-DC): discovering patients phenotypes and cell populations within a single Bayesian framework – Elie-Julien El Hachem – BMC Bioinformatics

February 24, 2023

Posted on by

Human and General Microbiome

Review: Gut microbiome lipid metabolism and its impact on host physiology – Brown et al. Cell Host & Microbe

Review: Modelling human immune responses using microbial exposures in rodents – Li and Baldridge. Nature Microbiology

Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis – Sun et al. Gut

An open label, non-randomized study assessing a prebiotic fiber intervention in a small cohort of Parkinson’s disease participants – Hall et al. Nature Communications

Antibiotic use and inflammatory bowel disease: number needed to harm? – Ludvigsson. Gut

Oral & Respiratory Microbiome

Oral mucosal breaks trigger anti-citrullinated bacterial and human protein antibody responses in rheumatoid arthritis – Brewer et al. Science Translational Medicine

Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease – Abotsi et al. Microbiome

Animal experiments

Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut – Zhang et al. Nature Microbiology

Microbe-mediated intestinal NOD2 stimulation improves linear growth of undernourished infant mice – Schwarzer et al. Science

Gamma-delta T cells modulate the microbiota and fecal micro-RNAs to maintain mucosal tolerance – Rezende et al. Microbiome

Phages and viruses

Review: Bacteriophage discovery to advance biotechnology and biotherapeutics – Mu and Lawley Nature Reviews Microbiology

Bioinformatics

Impact of microbial genome completeness on metagenomic functional inference – Eisenhofer et al. ISME

Pharokka: a fast scalable bacteriophage annotation tool – Bouras et al. Bioinformatics

Non Microbiome Picks

A systems immunology study comparing innate and adaptive immune responses in adults to COVID-19 mRNA and adenovirus vectored vaccines – Ryan et al. Cell Reports Medicine

Influenza-trained mucosal-resident alveolar macrophages confer long-term antitumor immunity in the lungs – Wang et al. Nature Immunology