Happy Friday! Today’s post features the rhizosphere of pinot noir grape plants, the impact of colostrum on the hindgut of dairy calves, and the microbial composition of the clownfish gut.

General microbiome

Review: Microbial forensics: new breakthroughs and future prospects – Oliveira – Applied Microbiology and Biotechnology

Pregnancy and early life

Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations – Ho – Nature Communications

Human oral microbiome

Review: Microbiological changes of the ageing oral cavity – Belibasakis – Archives of Oral Biology

Review: The oral microbiota: dynamic communities and host interactions – Lamont – Nature Reviews Microbiology

Human gut microbiome

Review: Non-alcoholic fatty liver disease and obesity: the role of the gut bacteria – Schwenger – European Journal of Nutrition

Impact of carbohydrate substrate complexity on the diversity of the human colonic microbiota – Chung – FEMS Microbiology Ecology

Oral iron exacerbates colitis and influences the intestinal microbiome – Mahalhal – PLoS One

Compositional and Temporal Changes in the Gut Microbiome of Pediatric Ulcerative Colitis Patients Are Linked to Disease Course – Schirmer – Cell Host & Microbe

Animal experiments

Colostrum feeding shapes the hindgut microbiota of dairy calves during the first 12 h of life – Song – FEMS Microbiology Ecology

Gut microbiome modulation during treatment of mucositis with the dairy bacterium Lactococcus lactis and recombinant strain secreting human antimicrobial PAP – Carvalho – Scientific Reports

Animal microbiome

Preprint: A simple microbiome in esophagus and gills of the European common cuttlefish, Sepia officinalis – Lutz – bioRxiv

Preprint: Feeding rapidly alters microbiome composition and gene transcription in the clownfish gut – Parris – bioRxiv

Profiling the airway in the macaque model of tuberculosis reveals variable microbial dysbiosis and alteration of community structure – Cadena – Microbiome

The gut bacteria across life stages in the synanthropic fly Chrysomya megacephala – Wang – BMC Microbiology

Multi-scale characterization of symbiont diversity in the pea aphid complex through metagenomic approaches – Guyomar – Microbiome

Microbial community and functions associated with digestion of algal polysaccharides in the visceral tract of Haliotis discus hannai: Insights from metagenome and metatranscriptome analysis – Nam – PLoS One

Critical Role for a Subset of Intestinal Macrophages in Shaping Gut Microbiota in Adult Zebrafish – Earley – Cell Reports

Plant, root, and soil microbiome

Soil acidification amendments change the rhizosphere bacterial community of tobacco in a bacterial wilt affected field – Shen – Applied Microbiology and Biotechnology

Geospatial variation in co‐occurrence networks of nitrifying microbial guilds – Jones – Molecular Ecology

Review: Elucidating Bacterial Gene Functions in the Plant Microbiome – Levy – Cell Host & Microbe

Amazonian deforestation and soil biodiversity – Franco – Conservation Biology

Metaproteomic characterization of Vitis vinifera rhizosphere – Bona – FEMS Microbiology Ecology

Water and extremophile microbiome

Exploring biogeographic patterns of bacterioplankton communities across global estuaries – Ghosh – MicrobiologyOpen

In situ responses of the sponge microbiome to ocean acidification – Kandler – FEMS Microbiology Ecology

Built environment

Stratification of microbial communities throughout a biological sulphate reducing up-flow anaerobic packed bed reactor, revealed through 16S metagenomics – Hessler – Research in Microbiology

Techniques

Preprint: Microbial contamination screening and interpretation for biological laboratory environments – Ning – bioRxiv

In today’s microbiome digest there are several interesting papers under animal experiments using mice, drosophila, mosquito vector and Ixodes scapularis ticks microbiome. Other important studies include the sinus swabs microbiome from chronic rhinosinusitis patients, lymph node microbiome from Crohn’s disease, intestinal microbiome profiling in psoriasis patients and a review which highlight on several common pitfalls for clinicians analyzing and interpreting the microbiome data. Enjoy reading.

General microbiome

Mucin Degradation Niche as a Driver of Microbiome Composition and Akkermansia Muciniphila Abundance in a Dynamic Gut Model is Donor Independent – Van Herreweghen Florence – FEMS Microbiology Ecology 

The human mesenteric lymph node microbiome differentiates between Crohn’s disease and ulcerative colitis – Miranda G Kiernan – Journal of Crohn’s and Colitis 

Review: Microbial enterotypes in personalized nutrition and obesity management – Lars Christensen – The American Journal of Clinical Nutrition 

Nasal microbiome

Relative abundance of nasal microbiota in chronic rhinosinusitis by structured histopathology – Hannah N. Kuhar BA – International Forum of Allergy and Rhinology

Respiratory microbiome

Pulmonary Metagenomic Sequencing Suggests Missed Infections in Immunocompromised Children – M S Zinter – Clinical Infectious Diseases

Human gut microbiome

Review: Microbiome 101: Studying, Analyzing, and Interpreting Gut Microbiome Data for Clinicians – Celeste Allaband – Clinical Gastroenterology and Hepatology

Increased relative abundance of Klebsiella pneumoniaecarbapenemase-producing Klebsiella pneumoniae within the gut microbiota is associated with risk of bloodstream infection in long-term acute care hospital patients – Teppei Shimasaki – Clinical Infectious Diseases

Intestinal microorganisms involved in colorectal cancer complicated with dyslipidosis – Shuwen Han – Cancer Biology and Therapy

Intestinal microbiota profiling and predicted metabolic dysregulation in psoriasis patients – Yi‐Ju Chen – Experimental Dermatology

Effects of products designed to modulate the gut microbiota on hyperlipidaemia – Xilong Deng – European Journal of Nutrition

Review: Bacterial antagonism in host-associated microbial communities – Leonor García-Bayona – Science 

Meconium microbiome associates with the development of neonatal jaundice – Tianyu Dong – Clinical and Translational Gastroenterology

Animal experiments

The effects of metabolic syndrome, obesity, and the gut microbiome on load-induced osteoarthritis – Guss JD – Osteoarthritis Cartilage

Microbial Quantity Impacts Drosophila Nutrition, Development, and Lifespan – Erin S.Keebaugh – iScience

Sex Differences in Pulmonary Responses to Ozone in Mice: Role of the Microbiome – Youngji Cho – American Journal of Respiratory Cell and Molecular Biology

Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota – Morgane Guégan – FEMS Microbiology Ecology

Effects of temperature on bacterial microbiome composition in Ixodes scapularis ticks – Santosh Thapa – MicrobiologyOpen

Intestinal anti-inflammatory effect of the probiotic Saccharomyces boulardii in DSS-induced colitis in mice: Impact on microRNAs expression and gut microbiota composition – Alba Rodríguez-Nogalesa – The Journal of Nutritional Biochemistry

Bioinformatics

Sequence clustering in bioinformatics: an empirical study – Quan Zou – Briefings in Bioinformatics

Techniques

Using non‐invasive metagenomics to characterize viral communities from wildlife – Laura M. Bergner – Molecular Ecology Resources

A lot of nutrition papers in todays digest! Along with some interesting papers on optimizing microbiome sample prep and modeling results. Also included is an article on gender bias in science. 

General microbiome

The microbiome and inborn errors of metabolism: Why we should look carefully at their interplay? – Colonetti K – Genetics and Molecular Biology

A Comparative Review on Microbiota Manipulation: Lessons From Fish, Plants, Livestock, and Human Research. – Brugman S – Frontiers in Nutrition

Human gut microbiome

Ectopic Fat Accumulation in Distinct Insulin Resistant Phenotypes; Targets for Personalized Nutritional Interventions. -Trouwborst I – Frontiers in Nutrition

The human gut pan-microbiome presents a compositional core formed by discrete phylogenetic units. -Aguirre de Cárcer D. – Scientific Reports

Microbiota-sensitive epigenetic signature predicts inflammation in Crohn’s disease. – Kelly D – JCI Insight

Human Oral microbiome

Child Weight Gain Trajectories Linked To Oral Microbiota Composition. – Crag SJC – Scientific Reports

Human Pregnancy microbiome

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome. – Goltsman DSA – Genome Research

Animal experiments 

Expansion of commensal fungus Wallemia mellicola in the gastrointestinal mycobiota enhances the severity of allergic airway disease in mice. – Skalski JH – PLoS Pathogens

Impact of Cross-Contamination Concentrations of Doxycycline Hyclate on the Microbial Ecosystem in an Ex Vivo Model of the Pig’s Cecum. – De Mulder T – Microbial Drug Resistance

Micromanaging Immunity in the Murine Host vs. the Mosquito Vector: Microbiota-Dependent Immune Responses to Intestinal Parasites. – Yordanova IA – Frontiers in Cellular and Infection Microbiology

The gut of the finch: uniqueness of the gut microbiome of the Galápagos vampire finch. – Michel AJ – Microbiome

Plant, root, and soil microbiome

A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments. – Vavourakis CD – Microbiome

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Techniques

Comparison of Fecal Collection Methods for Microbiome and Metabolomics Studies. – Wang Z – Frontiers in Cellular and Infection Microbiology

Bioinformatics

Modelling microbiome recovery after antibiotics using a stability landscape framework – – Liam P. Shaw – bioRxiv

Probiotics

The role of adjuvant probiotics to attenuate intestinal inflammatory responses due to cancer treatments. – Thomas M – Beneficial Microbes

Swathi’s non-microbiology picks

How female scientists can confront gender bias in the workplace  – Kendall Powell – Nature

Good morning! the publications from today’s microbiome digest covering the followings: Tick Microbiome, Chronic fatigue syndrome and alteration in the oral microbiome, CRC associated metabolites quantified from the faecal extracts, vaginal microbiome during cytolytic vaginosis, rumen and fecal bacterial community in high-production dairy cattle, and estimation of the expected variation in microbiome measurements (methodological research). Enjoy reading.

General microbiome

Thesis: Investigating the effects of the gut-associated microbial community on the growth of the eastern spruce budworm – Melbert Schwarz – Thesis

Tick Microbiome Characterization by Next-Generation 16S rRNA Amplicon Sequencing – Lisa Couper – Journal of Visualized Experiments: JoVE

Alcohol consumption increase susceptibility to pneumococcal pneumonia in a humanized murine HIV model mediated by intestinal dysbiosis – Derrick R.Samuelson – Alcohol 

Oral microbiome

Chronic fatigue syndrome patients have alterations in their oral microbiome composition and function – Taiwu Wang – PLOSONE

Human gut microbiome

Metabolite quantification of faecal extracts from colorectal cancer patients and healthy controls – Gwénaëlle Le Gall – Oncotarget

Vaginal microbiome

Characterization of the vaginal microbiome during cytolytic vaginosis using high-throughput sequencing – Haihong Xu – Wiley

Animal microbiome

High-production dairy cattle exhibit different rumen and fecal bacterial community and rumen metabolite profile than low-production cattle – Yingyu Mu – MicrobiologyOpen

Characterization of the Functional Changes in Mouse Gut Microbiome Associated with Increased Akkermansia muciniphila Population Modulated by Dietary Black Raspberries – Pengcheng Tu – ACS Omega

Plant, root, and soil microbiome

Dynamics of soil respiration and microbial communities: Interactive controls of temperature and substrate quality – Rana ShahbazAli – Soil Biology and Biochemistry

Microbial community structure and functions differ between native and novel (exotic-dominated) grassland ecosystems in an 8-year experiment – Aleksandra Checinska Sielaff – Plant and Soil

Impacts of heavy metals and soil properties at a Nigerian e-waste site on soil microbial community – Bo Jiang – Journal of Hazardous Material

Insight into Bacterial Community Diversity and Monthly Fluctuations of Medicago sativa Rhizosphere Soil in Response to Hydrogen Gas Using Illumina High-Throughput Sequencing – Zhiying Li – Current Microbiology

Extreme environmental microbiome

Bacterial diversity in snow from mid-latitude mountain areas: Alps, Eastern Anatolia, Karakoram and Himalaya – Roberto Sergio AZZONI – Annals of Glaciology

Water and extremophile microbiome

Characterization of bacterial and microbial eukaryotic communities associated with an ephemeral hypoxia event in Taihu Lake, a shallow eutrophic Chinese lake – Jian Cai – Environmental Science and Pollution Research

Inherent bacterial community response to multiple heavy metals in sediment from river-lake systems in the Poyang Lake, China – Hua Zhang – Ecotoxicology and Environmental Safety

Bioinformatics

Machine learning analysis of microbial flow cytometry data from nanoparticles, antibiotics and carbon sources perturbed anaerobic microbiomes – Abhishek S. Dhoble – Journal of Biological Engineering

Techniques

Methodology: Quantification of variation and the impact of biomass in targeted 16S rRNA gene sequencing studies – Jeffrey M. Bender – Microbiome

Good morning! Today’s Microbiome Digest will cover the general microbiome, skin microbiome, human gut microbiome, animal microbiome, a new technique NetoVIR for viral metagenomics, microbiome market and microbiome in the news. Enjoy reading.

General microbiome

Review: A comparative review on microbiota manipulation: lessons from fish, plants, livestock and human research – Sylvia Brugman – Frontiers in Nutrition

Skin microbiome

Antibacterial soap use impacts skin microbial communities in rural Madagascar – James J. Yu – PLOSONE

Skin microbiome of coral reef fish is highly variable and driven by host phylogeny and diet – Marlène Chiarello – Microbiome

Multi-site human microbiome

Identification and Visualization of a Distinct Microbiome in Ocular Surface Conjunctival Tissue – Jerome Ozkan – Immunology and Microbiology

Human gut microbiome

Age-Related Changes in the Gut Microbiota Influence Systemic Inflammation and Stroke Outcome – Monica S. Spychala – Annals of Neurology

Animal microbiome

A Comparative Study of Serum Biochemistry, Metabolome and Microbiome Parameters of Clinically Healthy, Normal Weight, Overweight, and Obese Companion Dogs – Genevieve M. Forster – Topics in Companion Animal Medicine

Synergetic action between the rumen microbiota and bovine health – Mohamed Zeineldin – Microbial Pathogenesis

Dietary corn bran improved the diversity of microbial communities and IL-10 production in weaned pigs – Ping Liu – Frontiers in Microbiology

Plant, root, and soil microbiome

Taxonomic and Functional Changes of Bacterial Communities in the Rhizosphere of Kimchi Cabbage After Seed Bacterization with Proteus vulgaris JBLS202 – Dipto Bhattacharyya – The Plant Pathology Journal

Water and extremophile microbiome

Preprint: Copper affects composition and functions of microbial communities in marine biofilms at environmentally relevant concentrations – Natàlia Corcoll – PeerJ

Bioinformatics

Machine learning meets genome assembly – Kleber Padovani de Souza – Briefings in Bioinformatics

Techniques

NetoVIR: Modular Approach to Customize Sample Preparation Procedures for Viral Metagenomics – Nádia Conceição-Neto – The Human Virome

Microbiome in the news

Gut Feeling: The Microbiome and Mental Health

Chronic malnutrition in children: A new gut microbial signature – Institut Pasteur

Microbiome market

Human Microbiome Market Expected to Grow at a CAGR of 20.9% During 2018 to 2025

Papers on the human virome, inflammatory bowel disease and new methods to understanding the microbiome. Also included is a documentary by Derek Muller (Veritasium) about Vitamins and host health for anyone interested in nutrition and the microbiome. 

Positions/Jobs

Microbiome Researcher – Clinical Microbiomics

General microbiome

Enteric virome of Ethiopian children participating in a clean water intervention trial – E Altan – PLoS One

Human respiratory microbiome

Association of nasal microbiome and asthma control in patients with chronic rhinosinusitis. – Yang HJ – Clinical and Experimental Allergy

In vivo imaging of bacterial colonization of the lower respiratory tract in a baboon model of Bordetella pertussis infection and transmission  – Thibaut Naninck – Scientific Reports

Human gut microbiome

Human Skin microbiome

Antibacterial soap use impacts skin microbial communities in rural Madagascar. – Yu JJ – PLoS One

Animal experiments 

Multi-strain probiotics enhance immune responsiveness and alters metabolic profiles in the New Zealand black-footed abalone (Haliotis iris) – R Grandiosa – Fish and Shellfish Immunology

Plant, root, and soil microbiome

Antibiotics and Antibiotic Resistance Genes in Bulk and Rhizosphere Soils Subject to Manure Amendment and Vegetable Cultivation – C Chen – Journal of Environmental Quality

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Technology

A High-Throughput Organoid Microinjection Platform to Study Gastrointestinal Microbiota and Luminal Physiology. – Williamson IA

An integrated, high-throughput strategy for multi-omic systems level analysis – Danielle B. Gutierrez – Journal of Proteome Research

Swathi’s non-microbiology picks

A new Documentary on Vitamins by Derek Muller – Vitamania