April 21, 2021

General microbiome

Assessment of the microbiome during bacteriophage therapy in combination with systemic antibiotics to treat a case of staphylococcal device infection – Mu et al. – Microbiome

Pregnancy and early life

A Microbiota-Directed Food Intervention for Undernourished Children – Chen et al. – The New England Journal of Medicine

Bacterial-fungal interactions in the neonatal gut influence asthma outcomes later in life – Boutin et al. – eLife

Human vaginal microbiome

[REVIEW]The effect of different contraceptive methods on the vaginal microbiome – Bastianelli et al. – Expert Review of Clinical Pharmacology

Human gut microbiome and virome

The Gut Microbiome in Progressive Multiple Sclerosis – Cox et al. – Annals of Neurology

Temporal landscape of human gut RNA and DNA virome in SARS-CoV-2 infection and severity – Zuo et al. – Microbiome

[REVIEW]The Gut Microbiome: a New Frontier in Musculoskeletal Research – Li et al. – Current Osteoporosis Reports

[REVIEW]Inflammation‐driven brain and gut barrier dysfunction in stress and mood disorders – Doney et al. – European Journal of Neuroscience

The gut microbiota is associated with clinical response to statin treatment in patients with coronary artery disease – Wang et al. – Atherosclerosis

[REVIEW]Dietary restrictions modulate the gut microbiota: Implications for health and disease – Schmidt and Lorentz – Nutrition Research

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

Altering the microbiome inhibits tumorigenesis in a mouse model of oviductal high-grade serous carcinoma – Chen et al. – Cancer Research

Screening of probiotic candidates in a simulated piglet small intestine in vitro model – Hansen et al. – FEMS Microbiology Letters

Animal microbiome (for animals in the wild)

Microbiome reduction and endosymbiont gain from a switch in sea urchin life history – Carrier et al. – PNAS

[PREPRINT]Evidence that faecal carriage of resistant Escherichia coli by 16-week-old dogs in the United Kingdom is associated with raw feeding and that E. coli from these dogs are shared with humans and cause opportunistic infections – Mounsey et al. – bioRxiv

Diversity structure of the microbial communities in the guts of four neotropical termite species – Vikram et al. – PeerJ

Alteration of gut microbiota with a broad‐spectrum antibiotic does not impair maternal care in the European earwig – van Meyel et al. – Journal of Evolutionary Biology

Food microbiology

The effects of vegetable pickling conditions on the dynamics of microbiota and metabolites – Sawada et al. – PeerJ

Techniques

[PREPRINT]Development of Microbiome Biomarkers for IgA: a Joint Modeling Approach – Sengupta et al. – bioRxiv

April 16, 2021

In today’s digest read about the presence/absence of ACBP orthologues in human gut metagenomes and how the gut microbiome links nutrition with cardiometabolic health, LEGO-based microscope, SIAMCAT for statistical inference of associations between microbial communities and host phenotypes, bacteriophage plaques size tool, and more. Check out a list of awesome webinars and courses. Happy Friday!

OPEN #NSURP2021 CALL for mentors and mentees: The National Summer Undergraduate Research Project – A community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the microbial sciences.

Microbiome in the news

*Microbiome research in general and business newspapers: How many microbiome articles are published and which study designs make the news the most? – Andreu Prados-Bo and Gonzalo Casino – PlosOne

General

Prokaryotic taxonomy and nomenclature in the age of big sequence data – Philip Hugenholtz – The ISME Journal

The metabolic network of the last bacterial common ancestor – Joana C. Xavier – Communications Biology

Techniques

*Designing a high-resolution, LEGO-based microscope for an educational setting – Bart Eduard Vos – bioRxiv

Genome-Based Targeted Sequencing as a Reproducible Microbial Community Profiling Assay – Jacquelynn Benjamino – mSphere

Gut microbiome

*Microbial ACBP/DBI-like genes are rare in the human gut microbiome and show no links with obesity – Andrew Maltez Thomas – Applied and Environmental Microbiology

The long-term genetic stability and individual specificity of the human gut microbiome – Lianmin Chen – Cell

Review: Emulating the gut–liver axis: Dissecting the microbiome’s effect on drug metabolism using multiorgan-on-chip models – Mara Lucchetti – Current Opinion in Endocrine and Metabolic Research

Urinary microbiome

The human urobiome – Linda Brubaker – Mammalian Genome

Urinary microbiota of women with recurrent urinary tract infection: collection and culture methods – Baylie R. Hochstedler – International Urogynecology Journal

Vaginal microbiome

Characterization of the first vaginal Lactobacillus crispatus genomes isolated in Brazil – Marcelle Oliveira de Almeida – PeerJ

Comparative Genome Analyses of Lactobacillus crispatus Isolates from Different Ecological Niches Reveal an Adaptation of This Species to the Human Vaginal Environment – Leonardo Mancabelli – Applied and Environmental Microbiology

Probiotics

Review: Lacticaseibacillus rhamnosus GR-1, a.k.a. Lactobacillus rhamnosus GR-1: Past and Future Perspectives – Mariya I.Petrova – Trends in Microbiology

Probiotic Lactobacillus sp. Strains Inhibit Growth, Adhesion, Biofilm Formation, and Gene Expression of Bacterial Vaginosis-Inducing Gardnerella vaginalis – Zhixiang Qian – Microorganisms

Oral microbiome

Dental biofilm microbiota dysbiosis is associated with the risk of acute graft-versus-host disease after allogeneic hematopoietic stem cell transplantation – Vitor Heidrich – medRxiv

Soil microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Carla Perez-Mon – Microbial Genomics

Phages and viruses

*Plaque Size Tool: an automated plaque analysis tool for simplifying and standardising bacteriophage plaque morphology measurements – Ellina Trofimova and Paul R Jaschke – bioRxiv

The gut virome of healthy children during the first year of life is diverse and dynamic – Blanca Taboada – PlosOne

Bioinformatics

Taxonomic analysis of metagenomic data with kASA – Silvio Weging – Nucleic Acids Research

*Microbiome meta-analysis and cross-disease comparison enabled by the SIAMCAT machine learning toolbox – Jakob Wirbel – Genome Biology

Review: Integrating pan-genome with metagenome for microbial community profiling – Chaofang Zhong – Computational and Structural Biotechnology Journal

Connecting structure to function with the recovery of over 1000 high-quality metagenome-assembled genomes from activated sludge using long-read sequencing – Caitlin M. Singleton – Nature Communications

Evaluation of the effects of library preparation procedure and sample characteristics on the accuracy of metagenomic profiles – Christopher Gaulke – bioRxiv

Democratising deep learning for microscopy with ZeroCostDL4Mic – Lucas von Chamier – Nature Communications

Webinars

Offered talks on Plasmids and Mobile Elements for 2021 – Plasmids around the globe – International Society for Plasmid Biology and Other Mobile Genetic Elements

Spring 2021 Microbiome Informatics webinars – OSU Center of Microbiome Science

EMBARK Spring Webinars – AMR focused webinars – EMBARK project

BISMiS Live – Microbial taxonomy: where are we now and where are we going? Iain Sutcliffe – Bergey’s Intl. Society for Microbial Systematics; registration here

Berkeley Lab Live Science – Exploring Earth – Berkeley Lab – April 23

Conferences

ISAPP 2021 Virtual Annual Meeting – International Scientific Association for Probiotics and Prebiotics – June 1–2

Courses

Open Online R Stream – Wolfgang Viechtbauer

RaukR: Advanced R for Bioinformatics Summer School – NBIS/SciLifeLab – June 14-24

April 14, 2021

General microbiome

[REVIEW]The microbiome and human cancer – Sepich-Poore et al. – Science

[PERSPECTIVE]A framework for microbiome science in public health – Wilkinson et al. – Nature Medicine

A framework for microbiome science in public health –

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Shaw et al. – Science Advances

Human gut microbiome

[REVIEW]Immune System, Microbiota, and Microbial Metabolites: The Unresolved Triad in Colorectal Cancer Microenvironment – Hanus et al. – Front. Immunol.

[REVIEW]Microbiome and colorectal cancer: A review of the past, present, and future – Johns & Petrelli – Surgical Oncology

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

Microbiota-derived short chain fatty acids modulate microglia and promote Aβ plaque deposition – Colombo et al. – eLife

Intestinal microbiota drives cholestasis-induced specific hepatic gene expression patterns – Juanola et al.

Animal microbiome (for animals in the wild)

When your host shuts down: larval diapause impacts host-microbiome interactions in Nasonia vitripennis – Dittmer & Brucker – Microbiome

Plant, root, and soil microbiome

Gut microbiota-derived inosine from dietary barley leaf supplementation attenuates colitis through PPARγ signaling activation – Li et al. – Microbiome

Important ecophysiological roles of non-dominant Actinobacteria in plant residue decomposition, especially in less fertile soils – Bao et al. – Microbiome

Rhizosphere community selection reveals bacteria associated with reduced root disease – Yin et al. – Microbiome

Shotgun metagenomics reveals distinct functional diversity and metabolic capabilities between 12 000-year-old permafrost and active layers on Muot da Barba Peider (Swiss Alps) – Perez-Mon – Microbioal Genomics

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

[PREPRINT]The Polar Night Shift: Annual Dynamics and Drivers of Microbial Community Structure in the Arctic Ocean – Wietz et al. – bioRxiv

Seafloor Incubation Experiment with Deep-Sea Hydrothermal Vent Fluid Reveals Effect of Pressure and Lag Time on Autotrophic Microbial Communities – Fortunato et al. – Environmental Microbiology

Plasmids

[PREPRINT]Plasmid fitness costs are caused by specific genetic conflicts – Hall et al. – bioRxiv

Bioinformatics

[PREPRINT]Comprehensive benchmarking of tools to identify phages in metagenomic shotgun sequencing data – Ho, Millard & van Schaik – bioRxiv

April 07, 2021

General microbiome

Primate phageomes are structured by superhost phylogeny and environment – Gogarten et al. – PNAS

Fungal‐induced glycolysis in macrophages promotes colon cancer by enhancing innate lymphoid cell secretion of IL‐22 – Zhu et al. – The EMBO Journal

A method for detection of SARS-CoV-2 RNA in healthy human stool: a validation study – Coryell et al. – The Lancet Microbe

The Ocular Microbiome and Microbiota and their Effects on Ocular Surface Pathophysiology and Disorders – Aragona et al. – Survey of Ophthalmology

Human oral microbiome

Multi-dimensional study of the oral microbiome, metabolite, and immunologic environment in peanut allergy – Ho et al. – Journal of Allergy and Clinical Immunology

Human skin microbiome

Temporal Variation in Staphylococcus aureus Protein A Genotypes from Nose and Skin in Atopic Dermatitis Patients – van Mierlo et al. – Dermatology

Sex‐Based Differences in Fecal Short‐Chain Fatty Acid and Gut Microbiota in Irritable Bowel Syndrome Patients – Sun et al. – Journal of Digestive Diseases

Human gut microbiome

[REVIEW]Ecological and evolutionary responses to antibiotic treatment in the human gut microbiota – Pennycook & Scanlan – FEMS Microbiology Reviews

Animal microbiome (for animals in the wild)

The Fecal and Serum Metabolomics of Giant Pandas Based on Untargeted Metabolomics – Yang et al. – Zoological Scienc

Microbes in space

Astrobiology of life on Earth – Hallsworth et al. – Environmental Microbiology
Mars’ surface is not universally biocidal – Hallsworth – Environmental Microbiology

Bioinformatics

Draft Genome Sequences and Antimicrobial Profiles of Three Staphylococcus epidermidis Strains from Neonatal Blood Samples – Afeke et al. – Microbiology Resource Announcements

CoCoNet: An Efficient Deep Learning Tool for Viral Metagenome Binning – Arisdakessian et al. – Bioinformatics

Techniques

Rank normalization empowers a t-test for microbiome differential abundance analysis while controlling for false discoveries – Davis, Huang & Wang – Briefings in Bioinformatics

Discovering multiple types of DNA methylation from bacteria and microbiome using nanopore sequencing – Tourancheau et al. – Nature Methods

April 1, 2021

General microbiome

Viral genomic, metagenomic and human transcriptomic characterization and prediction of the clinical forms of COVID-19 – Rodrigez et al. – PLOS Pathogens

A multiomics approach to identify host-microbe alterations associated with infection severity in diabetic foot infections: a pilot study – Radzieta – et al. – NPJ Biofilms and Microbiomes

Pregnancy and early life

Interactions between gut microbiota and metabolites modulate cytokine network imbalances in women with unexplained miscarriage – Liu et al. – NPJ Biofilms and Microbiomes

Developmental trajectory of the healthy human gut microbiota during the first 5 years of life – Roswall et al. – Cell Host & Microbiome

Human gut microbiome

Compositional change of gut microbiome and osteocalcin expressing endothelial progenitor cells in patients with coronary artery disease – Toya et al. – PLOS One

Stool metabolome-microbiota evaluation among children and adolescents with obesity, overweight, and normal-weight using 1H NMR and 16S rRNA gene profiling – Jaimes et al. – PLOS One

Gut dysbiosis and mortality in hemodialysis patients – Lin et al. – NPJ Biofilms and Microbiomes

[REVIEW]The Interplay between Diet, Gut Microbes, and Host Epigenetics in Health and Disease – Shock et al. – The Journal of Nutritional Biochemistry

[REVIEW]Circadian rhythms and the gut microbiome synchronize the host’s metabolic response to diet – Lopez et al. – Cell Metabolism

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

Meta-analysis identifies the effect of dietary multi-enzyme supplementation on gut health of pigs – Ramani et al. – Scientific Reports

Silicon-containing water intake confers antioxidant effect, gastrointestinal protection, and gut microbiota modulation in the rodents – Wu et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae) – Ting et al. – bioRxiv

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

Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake – Ahmad et al. – PLOS One

Geochemical and metagenomics study of a metal-rich, green-turquoise-coloured stream in the southern Swiss Alps – Buetti-Dinh – PLOS One

Phages and viruses

[REVIEW]The human virome: assembly, composition and host interactions – Liang & Bushman – Nature Reviews Microbiology

[PREPRINT]Diverse viruses carrying genes for microbial extremotolerance in the Atacama Desert hyperarid soil – Hwang et al. – bioRxiv

Bioinformatics

MCPdb: The bacterial microcompartment database – Ochoa et al. – PLOS One
[Twitter]97% identity cutoff applied on humans and related species – Matthew Hahn

Techniques

Single strain control of microbial consortia – Fedorec et al. – Nature Communications

Microbes and Art

A Cultural Triumph: Microbiology Student Makes A Petri Dish Masterpiece – McCammon – npr

March 31, 2021

Pregnancy and early life

Characterization of antimicrobial-resistant Gram-negative bacteria that cause neonatal sepsis in seven low- and middle-income countries – Sands et al. – Nature Microbiology

Human gut microbiome

The Gut Microbiome Is Altered in Postmenopausal Women With Osteoporosis and Osteopenia – Rettedal at al. – JBMR Plus
[Review]Ageing of the gut microbiome: potential influences on immune senescence and inflammageing – Conway & Duggal – Ageing Research Reviews

Human esophageal microbiome

Esophageal microbiome in active eosinophilic esophagitis and changes induced by different therapies – Laserna-Mendieta et al. – Scientific Reports

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

[PREPRINT]Establishment and Resilience of Transplanted Gut Microbiota in Aged Mice – Wang et al. – bioRxiv

Animal microbiome (for animals in the wild)

Termites Are Associated with External Species-Specific Bacterial Communities – Soukup et al. – Applied and Environmental Microbiology

Plant, root, and soil microbiome

Assessment of fungal diversity in soil rhizosphere associated with Rhazya stricta and some desert plants using metagenomics – Noor et al. – Archives of Microbiology

The temperature sensitivity of soil: microbial biodiversity, growth, and carbon mineralization – Wang et al. – The ISME Journal

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

Recovery of freshwater microbial communities after extreme rain events is mediated by cyclic succession – Shabarova et al. – Nature Microbiology

Techniques

Reduced metagenome sequencing for strain-resolution taxonomic profiles – Snipen et al. – Microbiome

March 28th, 2021

Hyvää Päivää from Helsinki, Finland ! Today’s digest contains quite a lot of different topics. If you are interested in marine microbiology and virology, I recommend taking a look at the paper by Gazitúa and collaborators. In this study they investigated the role of phages in shaping the metabolism metabolic networks along redox gradients associated with marine oxygen minimum zones. To do so, they investigated the phage contents in auxiliary metabolic genes involved in bacterial photosynthesis, central carbon metabolism, and nutrient cycling.  

Today’s non-microbiology pick is a web-platform, called Sysrev, built to aid in systematic evidence reviews. Sysrev contains thousands of Findable, Accessible, Iteroperable and Reusable (FAIR) datasets from a large variety of disciplines.

Have a great Sunday!


Human gut microbiome

Preprint: Fecal microbiome of children with norovirus gastroenteritis – Merces Hernandez et al. – bioRxiv 


Plant, root, and soil microbiome

Preprint: Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands – Wang et al. – bioRxiv 

Plant part and a steep environmental gradient predict plant microbial composition in a tropical watershed. – Bernard et al. – ISME J

Distribution patterns of Acidobacteriota in different fynbos soils – Conradie and Jacobs – PLOS

Water and extremophile microbiome

Preprint: Epidemiological dynamics of viral infection in a marine pico-eukaryote – Listmann et al. – bioRxiv  

Preprint: A deep-sea sulfate reducing bacterium directs the formation of zero-valent sulfur via sulfide oxidation – Liu et al. – bioRxiv

Preprint: Integrated multi-omics investigations reveal the key role of synergistic microbial networks in removing plasticizer di-(2-ethylhexyl) phthalate from estuarine sediments – Ting-Shyang Wei et al. – bioRxiv  

Time-series transcriptomics from cold, oxic subseafloor crustal fluids reveals a motile, mixotrophic microbial community – Seyler et al. – ISME J

Food microbiology

Preprint: Biofilm-forming capacity of Escherichia coli isolated from cattle and beef packing plants: relation to virulence attributes, stage of processing, antimicrobial interventions, and heat tolerance – Stanford et al. – bioRxiv


Phages and viruses

Potential virus-mediated nitrogen cycling in oxygen-depleted oceanic waters – Gazitúa et al. – ISME J

Bioinformatics

Umibato: estimation of time-varying microbial interaction using continuous-time regression hidden Markov model
Shion et al. – bioRxiv


My non-microbiology picks

Preprint: Sysrev: A FAIR Platform For Data Curation And Systematic Evidence Review – Bozada et al. – bioRxiv

March 27, 2021

Have a nice weekend! Today, in this Digest, we have an interesting review published in Science about microbiome and cancer. We have also articles about different conditions and the effect of the microbiome in the COVID19 vaccine-based immunity. More papers about: microbiome of wild animals,  cow microbiome and glyphosate,  anorexia microbiome in a mice model, and more!

Human and General Microbiome

Review: The microbiome and human cancer – Gregory D. Sepich-Poore – Science

Alterations in mucosa-associated microbiota in the stomach of patients with gastric cancer – Yilin Deng – Cellular Oncology 

Microbial genetic and transcriptional contributions to oxalate degradation by the gut microbiota in health and disease – Menghan Liu – eLife

The gut microbiome in subclinical atherosclerosis: a population-based multi-phenotype analysis – Sibo Zhu – Rheumatology

The microbiome in atopic patients and potential modifications in the context of the severe acute respiratory syndrome coronavirus 2 pandemic – Euna Lee – Current Opinion in Allergy and Clinical Immunology

An observational study of anaerobic bacteria in cystic fibrosis lung using culture dependant and independent approaches – Claudie Lamoureux – Scientific Reports

The Role of Mucosal Immunity and Recombinant Probiotics in SARS-CoV2 Vaccine Development – Shima Moradi-kalbolandi – Probiotics and Antimicrobial Proteins

Propionate catabolism by CD-associated adherent-invasive E. coli counteracts its anti-inflammatory effect – Allison Agus – Gut Microbes

Metabolic Syndrome Cannot Mask the Changes of Fecal Microbiota Compositions Caused by Primary Hepatocellular Carcinoma – Jiajia Ni – Letters in Applied Microbiology

Mendelian Randomization Analysis Reveals Causal Effects of the Human Gut Microbiota on Abdominal Obesity – Qian Xu – The Journal of Nutrition

Animal Microbiome

Diversity and functional landscapes in the microbiota of animals in the wild – Doron Levin – Science

Preliminary functional analysis of the subgingival microbiota of cats with periodontitis and feline chronic gingivostomatitis – Marjory Xavier Rodrigues – Scientific Reports

No hints at glyphosate-induced ruminal dysbiosis in cows – Fabian Billenkamp – npj Biofilms and Microbiomes 

Animal Models

Gut microbial communities from patients with anorexia nervosa do not influence body weight in recipient germ-free mice – Elaine M. Glenny – Gut Microbes

Environmental Microbiome

Invasive freshwater snails form novel microbial relationships – Laura Bankers – Evolutionary Applications

Preprint: Diversity and metagenome analysis of a hydrocarbon-degrading bacterial consortium from asphalt lakes located in Wietze, Germany – Michael O. Eze – Biorxiv

Built Environment

The Impacts of the Occupants on the Bacterial Communities of Classrooms – Zhou Feng – Current Microbiology 

Other

Meta-analysis methods for multiple related markers: Applications to microbiome studies with the results on multiple α-diversity indices – Hyunwook Koh – Statistics in Medicine

March 26, 2021

Good morning from New Jersey! Tons of papers to share with you today, including three about the role of the microbiome in COVID-19 and multiple new analysis tools and techniques.

Human respiratory microbiome

Functional profiling of COVID-19 respiratory tract microbiomes, Niina Haiminen et al., Scientific Reports

[Preprint] Mild CF Lung Disease is Associated with Bacterial Community Stability, Thomas H. Hampton et al., bioRxiv

Human skin microbiome

[Preprint] On-person adaptive evolution of Staphylococcus aureus during atopic dermatitis increases disease severity, Felix M. Key et al., bioRxiv

Human gut microbiome

[Mini-Review] The Unique Impact of COVID-19 on Human Gut Microbiome Research, Ella Burchill et al., Frontiers in Medicine

Variability in digestive and respiratory tract Ace2 expression is associated with the microbiome, Koester and Li et al., PLOS ONE

[Review] Towards a mechanistic understanding of reciprocal drug–microbiome interactions, Michael Zimmermann et al., Molecular Systems Biology

[Review] The Microbiome Meets Nanotechnology: Opportunities and Challenges in Developing New Diagnostic Devices, Celia Fuentes‐Chust et al., Advanced Materials

[Preprint] The capacity to produce hydrogen sulfide (H2S) via cysteine degradation is ubiquitous in the human gut microbiome, Domenick J Braccia et al., bioRxiv

Model experiments

[Preprint] Species richness determines C. difficile invasion outcome in synthetic human gut communities, Susan Hromada et al., bioRxiv

Gut microbiota determines the social behavior of mice and induces metabolic and inflammatory changes in their adipose tissue, Oryan Agranyoni et al., npj Biofilms and Microbiomes

Improvement of loperamide-induced slow transit constipation by Bifidobacterium bifidum G9-1 is mediated by the correction of butyrate production and neurotransmitter profile due to improvement in dysbiosis, Yutaka Makizaki et al., PLOS ONE

Animal microbiome

A Preliminary Comparison on Faecal Microbiomes of Free-Ranging Large Baleen (Balaenoptera musculus, B. physalus, B. borealis) and Toothed (Physeter macrocephalus) Whales, Stefanie P. Glaeser et al., Microbial Ecology

Host–microbial systems as glass cannons: Explaining microbiome stability in corals exposed to extrinsic perturbations, Courtney M. Dunphy et al., Journal of Animal Ecology

Fish predation on corals promotes the dispersal of coral symbionts, Carsten G. B. Grupstra et al., Animal Microbiome

Plant, root, and soil microbiome

Global analysis of the apple fruit microbiome: Are all apples the same?, Ahmed Abdelfattah et al., Environmental Microbiology

Evaluating domestication and ploidy effects on the assembly of the wheat bacterial microbiome, Wipf and Coleman-Derr, PLOS ONE

Water and extremophile microbiome

[Preprint] Uncharted biosynthetic potential of the ocean microbiome, Lucas Paoli et al., bioRxiv

The microbiome of the Black Sea water column analyzed by shotgun and genome centric metagenomics, Pedro J. Cabello-Yeves et al., Environmental Microbiome

Revealing taxon-specific heavy metal-resistance mechanisms in denitrifying phosphorus removal sludge using genome-centric metaproteomics, Yuan Lin et al., Microbiome

Bioinformatics

Forensic Microbiome Database: A Tool for Forensic Geolocation Meta-Analysis Using Publicly Available 16S rRNA Microbiome Sequencing, Singh and Clarke et al., Frontiers in Microbiology

ProgPerm: Progressive permutation for a dynamic representation of the robustness of microbiome discoveries, Liangliang Zhang et al., BMC Bioinformatics

Model-Based Microbiome Data Ordination: A Variational Approximation Approach, Yanyan Zeng et al., Journal of Computational and Graphical Statistics

Techniques

Blue poo: impact of gut transit time on the gut microbiome using a novel marker, Francesco Asnicar et al., Gut

Benchmarking DNA isolation kits used in analyses of the urinary microbiome, Lisa Karstens et al., Scientific Reports

Choice of library preparation affects sequence quality, genome assembly, and precise in silico prediction of virulence genes in shiga toxin-producing Escherichia coli, Julie Haendiges et al., PLOS ONE

March 24, 2021

Human gut microbiome

[OPINION]Targeting the Gut Microbiome to Mitigate Immunotherapy-Induced Colitis in Cancer – Chang et al – Trends in Cancer

Direct impact of commonly used dietary emulsifiers on human gut microbiota – Naimi et al. – Microbiome

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

[REVIEW]Establishing causality in Salmonella-microbiota-host interaction: The use of gnotobiotic mouse models and synthetic microbial communities – Stecher – International Journal of Medical Microbiology

Gut microbiota dysbiosis promotes age-related atrial fibrillation by lipopolysaccharide and glucose-induced activation of NLRP3-inflammasome – Zhang et al. – Cardiovascular Research

Animal microbiome (for animals in the wild)

Composition and structure of the skin microbiota of rorquals off the Eastern South Pacific – Toro et al. – FEMS Microbiology Ecology

Plant, root, and soil microbiome

[PREPRINT]Neural networks and extreme gradient boosting predict multiple thresholds and trajectories of microbial biodiversity responses due to browning – Fontaine et al. – bioRxiv

Comparative microbial antibiotic resistome between urban and deep forest environments – Zheng et al. – Environmental Microbiology Reports

Bioinformatics

[PREPRINT]Genomic characterization of three novel Desulfobacterota classes expand the metabolic and phylogenetic diversity of the Phylum – Murphy et al. – bioRxiv