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.

COVID-19

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.

COVID-19

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

April 29, 2020

Hello Everyone. Today the Microbiome Digest brings you the latest on Plant-microbial interaction together with a variety of your usual microbiome related research publications. Enjoy.

COVID-19:

Neuraxial anaesthesia and peripheral nerve blocks during the COVID-19 pandemic: a literature review and practice recommendations. – Uppal V. et al. – Anaesthesia.

General microbiome:

The link between autism spectrum disorder and gut microbiota: A scoping review – Nitschke A. et al. – Autism.

General microbiome:

Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? – Angebault C. et al. – PloS One.

Randomised clinical trial: faecal microbiota transplantation versus autologous placebo administered via colonoscopy in irritable bowel syndrome. – Lahtinen et al. – Aliment Pharmacol Ther.

High L-carnitine ingestion impairs liver function by disordering gut bacteria composition in mice. – Wu Q. et al. – J Agric Food Chem.

Plant, root, and soil microbiome:

Microbiome-Mediated Stress Resistance in Plants – Liu H et al. – Trends in Plant Science.

A plant genetic network for preventing dysbiosis in the phyllosphere – Chen T et al. – Nature.

Harnessing rhizosphere microbiomes for drought-resilient crop production – de Vries et al. – Science

Plant nutrient‐acquisition strategies drive topsoil microbiome structure and function – Bahram et al. – New Phytologist.

Impacts of directed evolution and soil management legacy on the maize rhizobiome – Schmidt JE et al. – Soil Biology and Biochemistry.

Environmental microbiome:

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. – Cyriaque V. et al. – FEMW Microbiol Ecol.

April 29, 2020

Hello Everyone. Today the Microbiome Digest brings you the latest on Plant-microbial interaction together with a variety of your usual microbiome related research publications. Enjoy.

COVID-19:

Neuraxial anaesthesia and peripheral nerve blocks during the COVID-19 pandemic: a literature review and practice recommendations. – Uppal V. et al. – Anaesthesia.

General microbiome:

The link between autism spectrum disorder and gut microbiota: A scoping review – Nitschke A. et al. – Autism.

General microbiome:

Combined bacterial and fungal targeted amplicon sequencing of respiratory samples: Does the DNA extraction method matter? – Angebault C. et al. – PloS One.

Randomised clinical trial: faecal microbiota transplantation versus autologous placebo administered via colonoscopy in irritable bowel syndrome. – Lahtinen et al. – Aliment Pharmacol Ther.

High L-carnitine ingestion impairs liver function by disordering gut bacteria composition in mice. – Wu Q. et al. – J Agric Food Chem.

Plant, root, and soil microbiome:

Microbiome-Mediated Stress Resistance in Plants – Liu H et al. – Trends in Plant Science.

A plant genetic network for preventing dysbiosis in the phyllosphere – Chen T et al. – Nature.

Harnessing rhizosphere microbiomes for drought-resilient crop production – de Vries et al. – Science

Plant nutrient‐acquisition strategies drive topsoil microbiome structure and function – Bahram et al. – New Phytologist.

Impacts of directed evolution and soil management legacy on the maize rhizobiome – Schmidt JE et al. – Soil Biology and Biochemistry.

Environmental microbiome:

Metal-induced bacterial interactions promote diversity in river-sediment microbiomes. – Cyriaque V. et al. – FEMW Microbiol Ecol.