September 29, 2020

Human gut microbiome

Gut microbiota and old age: Modulating factors and interventions for healthy longevity – Coman and Vodnar – Experimental Gerontology

Role of Gut Microbiome and Microbial Metabolites in Alleviating Insulin Resistance After Bariatric Surgery – Wang et al. – Obesity Surgery

Analysis of the infant gut microbiome reveals metabolic functional roles associated with healthy infants and infants with atopic dermatitis using metaproteomics – Kingkaw et al. – PeerJ

Effects of β-Lactam Antibiotics on Gut Microbiota Colonization and Metabolites in Late Preterm Infants – Lu et al. – Current Microbiology

Review article: how the intestinal microbiota may reflect disease activity and influence therapeutic outcome in inflammatory bowel disease – Caenepeel et al. – Alimentary Pharmacology and Therapeutics

Human oral microbiome

Comparative evaluation of microbial profiles of oral samples obtained at different collection time points and using different methods – Omori et al. – Clinical Oral Investigations

Human vaginal microbiome

Identification of Bacteriophages in the Vagina of Pregnant Women: A Descriptive Study – da Costa et al. – International Journal of Obstetrics and Gynaecology

Pregnancy and early life

Microbiome Understanding in Maternity Study (MUMS), an Australian prospective longitudinal cohort study of maternal and infant microbiota: study protocol – Susic et al. – BMJ Open

Plant, root and soil microbiome

Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression – Tae et al. – Microbiome *

Breeding selection imposed a differential selective pressure on the wheat root-associated microbiome – Kinnunen et al. – FEMS MICROBIOLOGY ECOLOGY

Temporal dynamics of bacterial communities during seed development and maturation – Chesneau et al. – FEMS MICROBIOLOGY ECOLOGY

Comparative analysis of rhizosphere soil physiochemical characteristics and microbial communities between rusty and healthy ginseng root – Bian et al. – Scientific Reports

Environmental microbiology

Community, Distribution, and Ecological Roles of Estuarine Archaea – Zou et al. – Frontier in Microbiology

Aerobic microbial communities in the sediments of a marine oxygen minimum zone – Bhattacharya et al. – FEMS MICROBIOLOGY LETTERS

Microbial prospection of communities that produce biosurfactants from the water column and sediments of the Gulf of Mexico – Morales-Guzman et al. – Biotechnology an dApplied Biochemistry

Animal experiments

Anatomy, immunology, digestive physiology and microbiota of the salmonid intestine: Knowns and unknowns under the impact of an expanding industrialized production – Bjørgen et al. – Fish & Shellfish Immunology

Disruption of ruminal homeostasis by malnutrition involved in systemic ruminal microbiota-host interactions in a pregnant sheep model – Xue et al. – Microbiome


Method development and validation for the quantification of organic acids in microbial samples using anionic exchange solid-phase extraction and gas chromatography-mass spectrometry – Heyen et al. – Analytical and Bioanalytical Chemistry

A novel universal primer pair for prokaryotes with improved performances for anammox containing communities – Mazzoli et al. – Scientific Reports

September 24, 2020.


Respiratory disease in cats associated with human-to-cat transmission of SARS-CoV-2 in the UK – Hosie et al. – bioRxiv

Human gut microbiome

The intestinal microbiome is a co-determinant of the postprandial plasma glucose response – Søndertoft et al. – PLOS ONE

Supplementation of a lacto-fermented rapeseed-seaweed blend promotes gut microbial- and gut immune-modulation in weaner piglets – Hui et al. – bioRxiv

Human vaginal microbiome

Changes of vaginal microbiota during cervical carcinogenesis in women with human papillomavirus infection – So et al. 2020 – PLOS ONE

Human fecal microbiome

Fecal microbiota transplantation in inflammatory bowel disease patients: A systematic review and meta-analysis – Caldeira et al. – PLOS ONE

Pregnancy and early life

Meconium microbiome and its relation to neonatal growth and head circumference catch-up in preterm infants – Terrazzan et al. – PLOS ONE

Plant, root and soil microbiome

Augmented Biodegradation of Textile Azo Dye Effluents by Plant Endophytes: A Sustainable, Eco-Friendly Alternative – Goud et al. 2020 – Current Microbiology

Regional Differences in the Structure of Juglans nigra Phytobiome Reflect Geographical Differences in Thousand Cankers Disease Severity – Onufrak et al. – Phytobiomes

Using the Microbiome Amplification Preference Tool (MAPT) to Reveal Medicago sativa-Associated Eukaryotic Microbes – Moccia et al. – Phytobiomes

Temporal variation in soil bacterial communities can be confounded with spatial variation – Hermans et al. – FEMS Microbial Ecology

A multi-omics approach to solving problems in plant disease ecology – Crandall et al. 2020 – PLOS ONE

Impact of Water Stress on Microbial Community and Activity in Sandy and Loamy Soils – Siebielec et al. – Agronomy

Animal experiments

The microbiota of the surface, dermis and subcutaneous tissue of dog skin – Garcia-Fonticoba et al. – Animal Microbiome

Host and altitude factors affect rumen bacteria in cattle – Wu et al. – Brazilian Journal of Microbiology

Environmental microbiology

Macroecological laws describe variation and diversity in microbial communities – Jacopo Grilli – Nature communications

Alpha-, beta-, and gamma-diversity of bacteria varies across habitats – Walters and Martiny – PLOS ONE

Linking microbial Sphagnum degradation and acetate mineralization in acidic peat bogs: from global insights to a genome-centric case study – James et al. – The ISME

September 18, 2020


Legal agreements: barriers and enablers to global equitable COVID-19 vaccine access – Phelan et al. -The Lancet

Science news

‘Scientific American’ Breaks 175 Years Of Tradition, Endorses A Presidential Nominee – NPR

Human microbiome

Early origin and global colonisation of foot-and-mouth disease virus – Aiewsakun et al. – Scientific Reports

Human gut microbiome

Alteration of Gut Microbiota in Patients With Epilepsy and the Potential Index as a Biomarker – Gong et al. – Frontiers in Microbiology

Plant, root, and soil microbiome

Amazonian soil metagenomes indicate different physiological strategies of microbial communities in response to land use change – Khan et al. – bioRxiv

Deciphering the Role of Trehalose in Tripartite Symbiosis Among Rhizobia, Arbuscular Mycorrhizal Fungi, and Legumes for Enhancing Abiotic Stress Tolerance in Crop Plants – Sharma et al. – Frontier in Microbiology

Animal experiments

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lobel et al. – Science

Investigation into the effect of divergent feed efficiency phenotype on the bovine rumen microbiota across diet and breed – McGovern et al. – Scientific Reports

August 20, 2020


Human organ chip-enabled pipeline to rapidly repurpose therapeutics during viral pandemics – Si et al. – bioRxiv

FDA approved calcium channel blockers inhibit SARS-CoV-2 infectivity in epithelial lung cells – Straus et al. – bioRxiv

Human oral microbiome

Removal of Dental Plaque by Ultrasonic Toothbrushes – Siddharth et al. – Journal of Critical Reviews

Cigarette smoking and opium use in relation to the oral microbiome in Iran – Zenei Wu et al. – Cancer Research

Animal experiments

Gut microbiome alterations induced by TBT exposure are associated with increased body weight, impaired glucose and insulin homeostasis and endocrine disruption in mice – Zhan et al. – Environmental Pollution

Poultry feeds carry diverse microbial communities that influence chicken intestinal microbiota colonisation and maturation – Haberecht et al. – AMB Express

Animal microbiome

Effects of Urbanization and Landscape on Gut Microbiomes in White-Crowned Sparrows – Berlow et al. – Microbial Ecology

Plant, root and soil microbiome

Plant–microbiome interactions: from community assembly to plant health – Trivedi et al. – Nature Reviews Microbiology *

Healthy soils for healthy plants for healthy humans: How beneficial microbes in the soil, food and gut are interconnected and how agriculture can contribute to human health – Heribert Hirt – EMBO reports

Chemical Ecology of Multitrophic Microbial Interactions: Plants, Insects, Microbes and the Metabolites that Connect Them – Ali et al. – Journal of Chemical Ecology

The role of land management and elevation in shaping soil microbial communities: Insights from the Central European Alps – Praeg et al. – Soil Biology and Biochemestry

Environmental microbiology

Ozone affects plant, insect, and soil microbial communities: A threat to terrestrial ecosystems and biodiversity – Agathokleous et al. – Science Advances *

Microplastics in a dam lake in Turkey: type, mesh size effect, and bacterial biofilm communities – Nihan Tavşanoğlu et al. – Environmental Science and Pollution Research


Assembly methods for nanopore‑based metagenomic sequencing: a comparative study – Latorre-Perez et al. – Scientific Reports

August 11, 2020

Human oral microbiome

A novel, simple, frequent oral cleaning method reduces damaging bacteria in the dental microbiota – Chhaliyil et al. – Journal of International Society of Preventive & Community Dentistry

Human gut microbiome

Rapid-Eye-Movement Sleep Behavior Disorder Exhibits Similar but Distinct Gut Dysbiosis Compared to Parkinson’s Disease – Nishiwaki et al. – bioRxiv

The Relationship between Choline Bioavailability from Diet, Intestinal Microbiota Composition, and Its Modulation of Human Diseases – Arias et al. – Nutrients.

Human fecal microbiome

Fecal microRNAs as Innovative Biomarkers of Intestinal Diseases and Effective Players in Host-Microbiome Interactions – Sashar et al. – Cancers

Animal experiments

An ambient temperature collection and stabilization strategy for canine microbiota studies – Lin et al. – Scientific Reports

Animal microbiome

Oral and vaginal microbiota in selected field mice of the genus Apodemus: a wild population study – Matějková et al. – Scientific Reports

Food microbiology

Barrel-Induced Variation in the Microbiome and Mycobiome of Aged Sour Ale and Imperial Porter Beer – Shayevitz et al. – Journal of the American Society of Brewing Chemist

Plant, root and soil microbiome

Influence of invasive earthworms (Amynthas spp.) on Wisconsin forest soil microbial communities and soil chemistry – Price-Christenson et al. – Soil Biology and Biochemestry

Field Exploitation of Multiple Functions of Beneficial Microorganisms for Plant Nutrition and Protection: Real Possibility or Just a Hope? – Kowalska et al. – Frontier in Microbiology

Composition and activity of nitrifier communities in soil are unresponsive to elevated temperature and CO2, but strongly affected by drought – Seneca et al. – The ISME journal

Environmental microbiome

Effects of the inoculum source, electron donor, and immobilization on the microbial community of sulfidogenic bioreactors – Marçal Ferraz et al. – Chemical Engineering Journal

Cryptic fungal diversity revealed in deep-sea sediments associated with whale-fall chemosynthetic ecosystems – Nagano et al. – Mycology


A survey on predicting microbe-disease associations: biological data and computational methods – Wen et al. – Briefings in Bioinoformatics

FORENSIC: an Online Platform for Fecal Source Identification – Roguet et al. – mSystems


Bacterial mock communities as standards for reproducible cytometric microbiome analysis – Cichocki et al. – Nature Protocols

Pikes peak – Rocky Mountain National Park, Colorado. (August 02, 2020).

August 3, 2020

Greetings from Colorado.
Today the Microbiome Digest brings you a variety of the latest microbiome related publications including brain, gut, fecal and oral microbiome, plant-microbial interactions and soil biodiversity. Enjoy!.


Rapid Inactivation of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) by Tungsten Trioxide-Based (WO3) Photocatalysis – Ghezzi et al. – bioRxiv

Human Microbiome: brain, gut, fecal and oral

This is the brain on probiotics – Annalisa M. VanHook – Science

Assessment of inter-laboratory variation in the characterization and analysis of the mucosal microbiota in Crohn’s disease and ulcerative colitis – Szamosi et al. -Frontiers in Microbiology

Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study – Huus et al. – Microbiome

Metapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity – Utter et al. – bioRxiv

Plant, root and soil microbiome

Evidence for the plant recruitment of beneficial microbes to suppress soil-borne pathogen – Liu et al. – bioRxiv

A Bacterial Effector Protein Hijacks Plant Metabolism to Support Pathogen Nutrition – Xian et al. – Cell Host & Microbe

Development and application of low-cost and eco-sustainable bio- stimulant containing a new plant growth-promoting strain Kosakonia pseudosacchari TL13 – Romano et al. – Frontiers in Microbiology

Environmental microbiology

Blind spots in global soil biodiversity and ecosystem function research – Guerra et al. – Nature Communications

Microbiome Diversity and Community-Level Change Points within Manure-based small Biogas Plants – Theuerl et al. – Microorganisms

June 29, 2020

Human microbiome

Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study. – Pan et al. – Psychiatry Research

A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents. – Holferson et al. – Scientific Reports

Gut microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. – Levy et al. – PNAS

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. – Hughes et al. – Nature Microbiology

Cancer and the microbiome. – Ashray Gunjur. The Lancet

Food microbiology

Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread – Reese et al. – mSphere

Plant, root and soil microbiome

Effects of zinc pollution and compost amendment on the root microbiome of a metal tolerant poplar clone. – Guarino et al. – Frontier in Microbioloy

New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. – Tang et al. – The ISME Journal

Language of plant-microbe-microbe interactions in rhizospheric ecosystems. – Khare et al. – Molecular Aspects of Plant Benefitial Microbes in Agriculture

Environmental microbiology

Editorial: Microbial Ecology in Reservoirs and Lakes. Zhang et al. – Frontier in Microbiology

Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. – Rodriguez and Duran – Frontiers in Bioengineering and Biotechnology.

May 30, 2020

Greetings from Colorado. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications including the human tumor microbiome by Nejman et al., microbial colonization in the neonatal gut microbiome by Wang and Dominguez-Bello, and drought effects on the millet root microbiome together with many more interesting papers. Enjoy.


Antimicrobial resistance in the age of COVID-19 – Editorial – Nature Microbiology

Metatranscriptomic Characterization of COVID-19 Identified A Host Transcriptional Classifier Associated With Immune Signaling – Zhang et al. – Clinical Infetious Diseases

General microbiome

Monitoring the microbiome for food safety and quality using deep shotgun sequencing – Beck et al. – bioRxiv

Fecal microbiota transplantation efficacy for Clostridium difficile infection: A trans-kingdom battle between donor and recipient gut microbiomes– Kazemian et al. – bioRxiv

Human microbiome

The human tumor microbiome is composed of tumor type–specific intracellular bacteria – Nejman et al. – Science*

Animal experiments

Pathogenesis, transmission and response to re-exposure of SARS-CoV-2 in domestic cats – Bosco-Lauth et al. – bioRxiv

The heart microbiome of insectivorous bats from Central and South Eastern Europe – Corduneanu et al. – bioRxiv

Gut microbiome

Microbial colonization alters neonatal gut metabolome – Wang and Dominguez-Bello – Nature Microbiology

Plant, root, and soil microbiome

Breeding for resistance: can we increase crop resistance to pathogens without compromising the ability to accommodate beneficial microbes? – Zuccaro and Langen – New Phytologist

Experimental assessment of tree canopy and leaf litter controls on the microbiome and nitrogen fixation rates of two boreal mosses – Jean et al. – New Phytologist

Drought Drives Spatial Variation in the Millet Root Microbiome – Simmons et al. – Frontiers in Plan Science*

Streptomyces’ scent attracts spore dispersers – Rohlfs – Nature Microbiology*

Diazotrophic bacteria from maize exhibit multifaceted plant growth promotion traits in multiple hosts – Higdon et al. – bioRxiv

May 29, 2020

Good Friday, everyone. Today the Microbiome Digest brings you a variety of the latest microbiome-related publications. Have a nice weekend.


Treatments in the COVID-19 pandemic: an update on clinical trials – Tao – Expert Opinion on Emerging Drug

Ozone Treatment for Elimination of Bacteria and SARS-CoV2 for Medical Environments – Westover et al. – bioRxiv

Coronavirus, as a source of pandemic pathogens – Konishi – bioRxiv

Nature news

Are women publishing less during the pandemic? Here’s what the data say

Coronavirus vaccine trials have delivered their first results — but their promise is still unclear

How to address the coronavirus’s outsized toll on people of colour

Human Microbiome

The role of gastric microbiota in gastric cancer – Stewart et al. – Gut Microbes

Ongoing Supplementation of Probiotics to Cesarean-Born Neonates during the First Month of Life may Impact the Gut Microbial – Yan et al. – Am J Perinatol

Animal experiments

Genetics but not intestinal microbiota determines the onset of systemic autoimmune disease in BXD2 mice – Hong et al. – The Journal of Immunology

Metabolic cooperation among commensal bacteria supports Drosophila juvenile growth under nutritional stress – Consuegra et al. – bioRxiv

Animal microbiome

Exploring the eukaryotic diversity in rumen of Indian camel (Camelus dromedarius) using 18S rRNA amplicon sequencing – Mishra et al. – Archives of Microbiology

Microbial metabolomics

IBD Microbial Metabolome: The Good, Bad, and Unknown – Sidebottom and Chang – Trends in Endocrinology & Metabolism

Environmental microbiology

Microbial Consortiums of Hydrogenotrophic Methanogenic Mixed Cultures in Lab-Scale Ex-Situ Biogas Upgrading Systems under Dierent Conditions of Temperature, pH and CO – Xu et al. – Microorganisms

Plant, root, and soil microbiome

Livestock grazing abandonment reduces soil microbial activity and carbon storage in a Mediterranean Dehesa – Oggioni et al. – Applie Soil Ecology

Halotolerant plant growth–promoting bacteria: Prospects for alleviating salinity stress in plants – Etesami & Glick – Environmental and Experimental Botany

Fertilization changes soil microbiome functioning, especially phagotrophic protists – Zhao et a. – Soil Biology and Biochemestry

Effect of combined application of organic and inorganic phosphatic fertilizers on dynamic of microbial biomass in semi-arid soil – Khosa et al.- Soil Science Annual

High levels of primary biogenic organic aerosols are driven by only a few plant-associated microbial taxa – Abdoulaye et al. – Atmospheric Chemestry & Physics

Complexity of bacterial and fungal network increases with soil aggregate size in an agricultural Inceptisol – Liao et al. – Applied Soil Ecology

Azole use in agriculture reduces Aspergillus fumigatus abundance but does not alter its population structure – Barber et al. – bioRxiv


Food microbiology

Novel Approaches to Minimising Mycotoxin Contamination – Jovita and Nunez – Toxins

Mentholation triggers brand-specific shifts in the bacterial microbiota of commercial cigarette products – Malayil et al. – Applied Microbial and Cell Physiology

May 23, 2020

Good Saturday, everyone. Today the Microbiome Digest brings you the latest on plant-microbial interaction and environmental microbiology together with a variety of your usual microbiome related publications. Enjoy!.

Human respiratory microbiome

A prevalent and culturable microbiota links ecological balance to clinical stability of the human lung after transplantation -Das et al.- bioRxiv

Human gut microbiome

A quantitative sequencing framework for absolute abundance measurements of mucosal and lumenal microbial communities -Barlow et al.- Nature Communications

Gut Microbiota and Disorders of the Central Nervous System – Vuotto et al.- Neuroscientist

Animal experiments

Intestinal fungi are causally implicated in microbiome assembly and immune development in mice– Erik van Tilburg Bernardes et al.- Nature Communications

Linking perturbations to temporal changes in diversity, stability, and compositions of neonatal calf gut microbiota: prediction of diarrhea -Ma et a.- ISME

Built environment

Continental-scale microbiome study reveals different environmental characteristics determining microbial richness and composition/quantity in hotel rooms -Fu et al.- mSystems

Environmental Microbiology

Extreme storms cause rapid, context-dependent shifts in nearshore subtropical bacterial communities -Ares et al.- bioRxiv

Mimicking climate warming effects on Alaskan soil microbial communities via gradual temperature increase – Ballhausen et al.- Scientific Reports

Plant, root, and soil microbiome

Deciphering the root endosphere microbiome of the desert plant Alhagi sparsifolia for drought resistance-promoting bacteria -Zhang et al.- Applied and

Drought and plant litter chemistry alter microbial gene expression and metabolite production -Malik et al.- ISME

Genome-scale metabolic reconstruction of the symbiosis between a leguminous plant and a nitrogen-fixing bacterium– DiCenzo et al.- Nature Communications