July 14, 2022

Today’s digest has multiple articles on statistical and bioinformatic techniques! Also included is a job ad from my research team, so check it out if you’re interested in gaining geomicrobiology research experience at a national laboratory.

Events and jobs

Our geomicrobiology research group at the National Energy Technology Lab – Pittsburgh is looking for a technician/researcher. Exact responsibilities are somewhat flexible depending on interest and education-level; we are accepting applications from current students at all levels as well as postdocs.

General microbiome

Mycobacteriophages: From Petri dish to patient – Hatfull – PLOS Pathogens

Animal microbiome

Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee – Wirta et al. – PLOS One

Plant, root, and soil microbiome

Patterns of microbial communities were shaped by bioavailable P along the elevation gradient of Shergyla Mountain, as determined by analysis of phospholipid fatty acids – Ba et al. – PLOS One

Preprint: Soil chemistry and soil history significantly structure oomycete communities in Brassicaceae crop rotations – Blakney et al. – bioRxiv

Community succession and straw degradation characteristics using a microbial decomposer at low temperature – Zhang et al. – PLOS One

Built Environment

Indoor air microbial load, antibiotic susceptibility profiles of bacteria, and associated factors in different wards of Arba Minch General Hospital, southern Ethiopia – Kayta et al. – PLOS One

Techniques

moreThanANOVA: A user-friendly Shiny/R application for exploring and comparing data with interactive visualization – Jiang et al. – PLOS One

Preparation of biological monolayers for producing high-resolution scanning electron micrographs – Mentor et al. – PLOS One

The accuracy of absolute differential abundance analysis from relative count data – Roche & Mukherjee – PLOS Computational Biology

AC-PCoA: Adjustment for confounding factors using principal coordinate analysis – Wang et al. – PLOS Computational Biology

Microbes in the news

The Art of Science: Students Participate in University’s First-Ever Bio-Art Class – Bernardi – Syracuse University News

March 18, 2021

Greetings from Pittsburgh!

Today’s digest has a lot of food and agriculture associated articles. Several articles focus on the effects of various pathogens on dairy cows, beef steers, and poultry breeds! For those of us who are more interested in plants, there is an article on biogas production from tomato waste and a preprint on how the microbial community of food waste changes during the composting process. Finally, I included a research article about social media during the pandemic since I’m sure I’m not the only one who has relied on it a little too heavily over the last year…

Happy reading!

General microbiome

Preprint: Toward quantifying the adaptive role of bacterial pangenomes during environmental perturbations – Conrad et al. – bioRxiv

BlueFeather, the singleton that wasn’t: Shared gene content analysis supports expansion of Arthrobacter phage Cluster FE – Demo et al. – PLOS ONE

Review: The gut microbiota–brain axis in behaviour and brain disorders – Morais et al. – Nature Reviews Microbiology

Preprint: Cross-species evolutionary rewiring in the enteric bacterium Campylobacter – Taylor et al. – bioRxiv

Human gut microbiome

Gut microbiota profiles in diarrheic patients with co-occurrence of Clostridioides difficile and Blastocystis – Vega et al. – PLOS ONE

Animal experiments

Preprint: Low pathogenic avian influenza virus infection retards colon microbiome diversification in two different chicken lines – Chrzastek et al. – bioRxiv

Preprint: Borrelia infection in rodent host has dramatic effects on the microbiome of ticks – Hamilton et al. – bioRxiv

Animal microbiome

Preprint: The discovery, distribution and diversity of DNA viruses associated with Drosophila melanogaster in Europe – Wallace et al. – bioRxiv

Plant, root, and soil microbiome

Effects of precipitation change and nitrogen addition on the composition, diversity, and molecular ecological network of soil bacterial communities in a desert steppe – Jia et al. – PLOS ONE

Preprint: Changes and composition of microbial community during aerobic composting of household food waste – Jin et al. – bioRxiv

Preprint: What’s under the Christmas tree? Soil acidification alters fir tree rhizosphere bacterial and eukaryotic communities, their interactions, and functional traits – Steven et al. – bioRxiv

A comparative analysis of biogas production from tomato bio-waste in mesophilic batch and continuous anaerobic digestion systems – Szilágyi et al. – PLOS ONE

Food microbiology

Red seaweed (Asparagopsis taxiformis) supplementation reduces enteric methane by over 80 percent in beef steers – Roque et al. – PLOS ONE

Prevalence and distribution of multilocus sequence types of Staphylococcus aureus isolated from bulk tank milk and cows with mastitis in Pennsylvania – Thomas et al. – PLOS ONE

Multidrug-resistant enterobacteria in newborn dairy calves in Germany – Waade et al. – PLOS ONE

Phages and viruses

Review: Viral and host heterogeneity and their effects on the viral life cycle – Jones et al. – Nature Review Microbiology

Bioinformatics

Dcmd: Distance-based classification using mixture distributions on microbiome data – Shestopaloff et al. – PLOS Computational Biology

Kara’s non-microbiology pick

Don’t put all social network sites in one basket: Facebook, Instagram, Twitter, TikTok, and their relations with well-being during the COVID-19 pandemic – Masciantonio et al. – PLOS ONE

February 9, 2021

Today’s updates in microbiome – iron homeostasis in host and gut bacteria, flavonol catabolism in gut bacteria, protocol for characterization of pulmonary microbiota, how single bacterial strain prevents GVHD and many more… happy reading!

General microbiome

Iron homeostasis in host and gut bacteria – a complex interrelationship – Yohannes Seyoum – Gut Microbes

α1-3Gal antigen in gut microbiota, a potential new environmental factor in multiple sclerosis – LéoBoussamet – Clinical Immunology

Human microbiome

Alterations in the gut bacterial microbiome in people with type 2 diabetes mellitus and diabetic retinopathy – Taraprasad Das – Scientific Reports

Discovery of an ene-reductase for initiating flavone and flavonol catabolism in gut bacteria – Gaohua Yang – Nature Communications

Animal microbiome

A single strain of Bacteroides fragilis protects gut integrity and reduces GVHD – M. Hanief Sofi – JCI Insight

Social behavior of musk deer during the mating season potentially influences the diversity of their gut microbiome – Jianmei Li​ – PeerJ

Low-dose exposure of glyphosate-based herbicides disrupt the urine metabolome and its interaction with gut microbiota – Jianzhong Hu – Scientific Reports

Cross-Feeding of a Toxic Metabolite in a Synthetic Lignocellulose-Degrading Microbial Community – Jessica A. Lee – Microorganisms

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – LeeMin-Ting – Journal of Lipid Research

Functional Foods

Shaping the Future of Probiotics and Prebiotics – Marla Cunningham – Trends in Microbiology

Utilizing the Food–Pathogen Metabolome to Putatively Identify Biomarkers for the Detection of Shiga Toxin-Producing E. coli (STEC) from Spinach – Snehal R. Jadhav – Metabolites

Clinical effects and gut microbiota changes of using probiotics, prebiotics or synbiotics in inflammatory bowel disease: a systematic review and meta-analysis – Xiao-Feng Zhang – European Journal of Nutrition

Diabetes-induced cardiomyopathy is ameliorated by heat-killed Lactobacillus reuteri GMNL-263 in diabetic rats via the repression of the toll-like receptor 4 pathway – Chung-Jen Chiang – European Journal of Nutrition

Water microbiome

Understanding structure/function relationships in nitrifying microbial communities after cross-transfer between freshwater and seawater – Blanca M. Gonzalez-Silva – Scientific Reports

The microbial dimension of submarine groundwater discharge:current challenges and future directions – Clara Ruiz-González- FEMS Microbiology Reviews

Estrogen induces shift in abundances of specific groups of the coral microbiome – Caren L. S. Vilela – Scientific Reports

Metabolic fingerprinting of the Antarctic cyanolichen Leptogium puberulum–associated bacterial community (Western Shore of Admiralty Bay, King George Island, Maritime Antarctica) – Jakub Grzesiak – Microbial Ecology

Techniques

Development of a robust protocol for the characterization of the pulmonary microbiota – Nathan Dumont-Leblond – Nature Communications

Microbes in news

Eating fat-rich foods as a child causes long-lasting changes in gut microbiome: Study – First post

Human Microbiome Market Set to Register Healthy CAGR During to 2026 – KSU The Sentinel Newspaper

July 26, 2020

General microbiome

No endospore formation confirmed in members of the phylum Proteobacteria – Polina Beskrovnaya – bioRxiv

Interbacterial competition and anti-predatory behavior of environmental Vibrio cholerae strains – Natalia C. Drebes Doerr – bioRxiv

The kleboxymycin biosynthetic gene cluster is encoded by several species belonging to the Klebsiella oxytoca complex – Preetha Shibu – bioRxiv

Plant, root, and soil microbiome

POPULATION GENOMICS REVEALS MOLECULAR DETERMINANTS OF SPECIALIZATION TO TOMATO IN THE POLYPHAGOUS FUNGAL PATHOGEN BOTRYTIS CINEREA – Alex Mercier – bioRxiv

Phages and viruses

Scientometric Trends for Coronaviruses and Other Emerging Viral Infections – Dima Kagan – bioRxiv

Bioinformatics

Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae – Liam P Shaw – bioRxiv

Techniques

Comparing DNA Extraction and 16s Amplification Methods for Plant-Associated Bacterial Communities – Cecelia Giangacomo – bioRxiv

Microrisk Lab: an online freeware for predictive microbiology – Yangtai Liu – bioRxiv

Microbes in the news 

Human microbiome project paved way for poultry research – WATTAgNet

Microbes on the market

SeqBiome’s clients already include Nestlé, Mars Petcare, Atlantia and Microbion, among others. – Silicon Republic

Global Human Microbiome Sequencing Market 2020 Industry Research Strategy, Outlook and Product Development to 2025 – Bandera County Courier

July 1, 2020

Greetings Everyone,
I want to began the month of July on a note that diversity is the basis for life. I can’t think of anything better to teach us about diversity, co-existence, and evolution than the fascinating Microbiome.
The microbiome affects us right from our birth till the end affecting our mental as well as physical health. The microbiome exhibits all sorts of differences in shape, size, color, metabolic functions in order to sustain life.
Much to learn from these tiny beings!!!!
Today’s Digest comprises of some interesting studies about effect of microbiome on chemotherapy and studies on tumor microbiome. It also includes articles exploring genetics of gut microbiome and the role of microbiome in inflammatory bowel disease. Additionally has a news article about taking microbiome therapies to clinical trials.
Hope you enjoy reading today’s digest!!
“Life on earth is such a good story you cannot afford to miss the beginning… Beneath our superficial differences we are all of us walking communities of bacteria. The world shimmers, a pointillist landscape made of tiny living beings”. – Lynn Margulis


General microbiome
Human Microbiota and Effectiveness of Cancer Chemotherapy – Shvets et al – Experimental Oncology

Immunity to commensal skin fungi promotes psoriasiform skin inflammation – Hurabielle et al – PNAS

Human Tumor microbiome
*Perspective: Probing the tumor micro(b)environment – Atreya et al – Science

Human Eye microbiome
Review: Current Knowledge on the Human Eye Microbiome: A Systematic Review of Available Amplicon and Metagenomic Sequencing Data – Delbeke et al – Acta Ophthalmologica

Human nearly-sterile sites (blood, organs, brain)
Blood Bacterial Profiles Associated with HIV Infection and Immune Recovery – Serranno-Villar et al – The Journal of Infectious Diseases

Human gut microbiome
*Genetics of human gut microbiome composition – Kurilshikov et al – bioRxiv

Review: The microbiome in inflammatory bowel diseases: from pathogenesis to therapy – Liu et al – Protein&Cell


Built environment
Vertical Stratification in Urban Green Space Aerobiomes – Robinson et al – bioRxiv

Food microbiology
Food and mood: how do diet and nutrition affect mental wellbeing? – Firth et al – BMJ


Bioinformatics
DRAM for distilling microbial metabolism to automate the curation of microbiome function – Shaffer et al – bioRxiv

Techniques
MetaRibo-Seq measures translation in microbiomes – Fremin et al – Nature Communications


Microbes on the market
Enterome Secures €46M to Take Microbiome Therapies to Clinical Trials – Helen Albert – Labiotech.eu

Human Microbiome Therapeutics Market Research: Global Status & Forecast by Geography, Type & Application (2016-2026)

June 22, 2020

General microbiome
Impact of feeding and stirring regimes on the internal stratification of microbial communities in the fermenter of anaerobic digestion plants – Robert Heyera – Bioresource Technology

Human microbiome
REVIEW: Role of the Microbiome in Allergic Disease Development – Andrea C. Aguilera, – Pediatric Allergy and Immunology

Optimization and standardization of the culturomics technique for human microbiome exploration – Ami Diakite – Scientific Reports

Human skin microbiome
The microbiome of diabetic foot ulcers: a comparison of swab and tissue biopsy wound sampling techniques using 16S rRNA gene sequencing – J. Travis – BMC Microbiology

Human gut microbiome
Interpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection – Salma Alavi – Cell

EDITORIAL: Gut microbes effects on host metabolic alterations in health and disease – Suzana D. Savkovic – Gut Microbes

Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study – Mohammad Tahseen Al Bataineh – Scientific Reports

Alterations in the Gut Microbiome in the Progression of Cirrhosis to Hepatocellular Carcinoma – Yelena Lapidot – mSystems

Human respiratory microbiome
Taxonomic diversity of sputum microbiome in lung cancer patients and its relationship with chromosomal aberrations in blood lymphocytes – V. G. Druzhinin – Scientific Reports

Pregnancy and early life
Human milk microbiota development during lactation and its relation to maternal geographic location and gestational hypertensive status – Yi Wan – Gut Microbes

Maternal Microbiota, Cortisol Concentration, and Post-PartumWeight Recovery Are Dependent on Mode of Delivery – Marta Selma-Royo – Nutrients

Human ancient microbiome
Analysis of oral microbiome from fossil human remains revealed the significant differences in virulence factors of modern and ancient Tannerella forsythia – Anna Philips – BMC Genomics

Animal experiments
Zebrafish microbiome studies make waves – Keaton Stagaman – Lab Animal

Animal microbiome
An Insight into Diversity and Functionalities of Gut Microbiota in Insects – Shengchen Wang – Current Microbiology

Plant, root, and soil microbiome
Microbial assimilation dynamics differs but total mineralization from added root and shoot residues is similar in agricultural Alfisols – Yingde Xu – Soil Biology and Biochemistry

Effects of increasing concentrations of unamended and gypsum modified bauxite residues on soil microbial community functions and structure – A mesocosm study – Camille Fourrier – Ecotoxicology and Environmental Safety

Microbiome approaches provide the key to biologically control postharvest pathogens and storability of fruits and vegetables – Peter Kusstatscher – FEMS Microbiology Ecology

Variations of rhizospheric soil microbial communities in response to continuous Andrographis paniculata cropping practices – Junren Li – Botanical Studies

Seed Metabolism and Pathogen Resistance Enhancement in Pisum sativum During Colonization of Arbuscular Mycorrhizal Fungi: An Integrative Metabolomics-Proteomics Approach – Nima Ranjbar Sistani – Frontiers in Plant Science

Water microbiome
Differential Responses of a Coastal Prokaryotic Community to Phytoplanktonic Organic Matter Derived from Cellular Components and Exudates – Hiroaki Takebe – Microbes and Environments

Built environment
MINI-REVIEW: Microorganisms populating the water-related indoor biome – Monika Novak Babič – Applied Microbiology and Biotechnology

Pre-print
Shotgun metagenomics reveals signicant gut microbiome features in different grades of acute pancreatitis – Shanshan Yu – Research Square

Characteristics of Esophagus Flora in Patients with Esophageal Squamous Cell Carcinoma in Central China – Shuixiang He – Research Square

Can root-associated fungi mediate the impact of abiotic conditions on the growth of a High Arctic herb? – Magdalena Wutkowska – bioRxiv

Microbes on the market
Finch Therapeutics Announces Positive Topline Results from Randomized Controlled Trial of CP101, an Oral Microbiome Drug, for the Prevention of Recurrent C. difficile Infection – Finch Therapeutics

Microbes in the news
Gut reaction: How the gut microbiome may influence the severity of COVID-19 – Shirin Moossavi – The Conversation

April 21, 2020

Hello all from another new Microbiome Digest volunteer! This post is coming to you straight from the heart of New York City – being surrounded everywhere by COVID-19 (and related research!), it’s been good to get back into the microbiome world 🙂 I love all things microbiology but am partial to bacteria, especially multidrug-resistant pathogens and communities involved in biological nutrient removal/recovery from waste.

Today’s roundup is heavy on the soil and environmental microbiomes and some interesting preprints, with some unique finds – indigenous yeasts in winemaking, gut microbiomes after dietary interventions in adult dogs, and much more!


Human gut microbiome

Characterization of Gut Microbiota in Hospitalized Patients with Clostridioides difficile Infection – Bahareh Vakili – Current Microbiology


Animal experiments
Genetic and metabolic links between the murine microbiome and memory – Jian-Hua Mao – Microbiome

A human-origin probiotic cocktail ameliorates aging-related leaky gut and inflammation via modulating microbiota-taurine-tight junction axis
Shokouh Ahmadi – JCI Insight

Animal microbiome

Preprint: CoproID predicts the source of coprolites and paleofeces using microbiome composition and host DNA content – Maxime Borry – bioRxiv

Phylogenetic analysis of intestinal microbiota reveals novel Mycoplasma phylotypes in salmonid species – Brenda Mora-Sánchez – Microbial Pathogenesis

Rapid Reconstitution of the Faecal Microbiome after Extended Diet-Induced Changes Indicate a Stable Gut Microbiome in Healthy Adult Dogs – David Allaway – Applied and Environmental Microbiome

Plant, root, and soil microbiome

Review: Harnessing rhizosphere microbiomes for drought-resilient crop production – Franciska T. de Vries – Science

Book Chapter: Endophytic Actinomycetes-Mediated Modulation of Defense and Systemic Resistance Confers Host Plant Fitness Under Biotic Stress Conditions – Waquar Akhter Ansari – Microbial Versatility in Varied Environments

Elevated CO2 mitigates the negative effect of CeO2 and Cr2O3 nanoparticles on soil bacterial communities by alteration of microbial carbon use – Jipeng Luo – Environmental Pollution

Periodic waterlogging consistently shapes agricultural soil microbiomes by promoting specific taxa – Florian Gschwend – Applied Soil Ecology

Food microbiology

Review:Indigenous yeasts: Emerging Trends and Challenges in winemaking – Iliada K. Lappa – Current Opinion in Food

Ecology of lactobacilli present in Italian cheeses produced from raw milk
Christian Milani – Applied and Environmental Microbiology


Probiotics / prebiotics
Probiotic supplementation improves cognitive function and mood with changes in gut microbiota in community-dwelling elderly: A randomized, double-blind, placebo-controlled, multicenter trial – Chong-Su Kim – The Journals of Gerontology

Phages and viruses
Intestinal microbiome‐macrophage crosstalk contributes to cholestatic liver disease by promoting intestinal permeability – Anna Isaacs-Ten – Hepatology

Bioinformatics
Preprint: hogwash: Three Methods for Genome-Wide Association Studies in Bacteria – Katie Saund – bioRxiv

Mycobiome

Preprint: Mycobiome analysis in fungal Infected formalin-fixed and paraffin-embedded tissues for identification of pathogenic fungi: A pilot study – Taebum Lee – bioRxiv

Host-Pathogen Interactions
Preprint: Human GBP1 differentially targets Salmonella and Toxoplasma to license recognition of microbial ligands and caspase-mediated death – Daniel Fisch – bioRxiv

Preprint: Mechanical competition triggered by innate immune signaling drives the collective extrusion of bacterially-infected epithelial cells – Effie E. Bastounis – bioRxiv


Microbes on the market

Genome & Company receives FDA IND clearance for GEN-001, its first anti-cancer microbiome therapeutic (Press Release, BioSpace)

April 7, 2020

Hi everyone! This is my first contribution to the daily digest, and I’ll follow others’ lead by starting with the latest preprints concerning Covid-19. Away from the ongoing pandemic, some of the highlights include a look at how commensal gut microbes interact with pathogens, and an insight into deep sea oceanic crust microbiomes.

It seems to be a relatively quiet day today, so I’ve included an article from the University of Bristol which looks at how nanoscopic pillars on the surface of some insect wings protect them against bacteria. Perhaps only loosely a microbiome paper, but it’s worth a read for its electron microscopy alone!

COVID-19

Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor – Lan et al. – Nature

Preprint: Atazanavir inhibits SARS-CoV-2 replication and pro-inflammatory cytokine production – Fintelman-Rodrigues et al.

Preprint: Amantadine disrupts lysosomal gene expression; potential therapy for COVID19 – Smieszek et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Mantlo et al.

Human gut microbiome

Dissecting individual pathogen-commensal interactions within a complex gut microbiota community – Hassall and Unnikrishnan

Animal microbiome

Antibacterial effects of nanopillar surfaces are mediated by cell impedance, penetration and induction of oxidative stress – Jenkins et al. – Nature Communications

Water and extremophile microbiome

Deep microbial proliferation at the basalt interface in 33.5–104 million-year-old oceanic crust – Suzuki et al.Communications Biology

Food microbiology

How does the microbiome impact pig health? – Sarah Mikesell – The Pig Site

Microbes in the news

Lifestyle trumps geography in determining makeup of gut microbiomeEurekAlert!

Microbes on the market

Gilead taps Second Genome for microbiome biomarker help in a potential $1.5B deal – Connor Hale – FierceBiotech.com

March 24, 2020

Today’s Digest features a study to use engineered Acinetobacter to boost host immunity against bacterial pneumonia, and a review on the relationship between plant-microbe symbiosis and agriculture.The coronavirus is probably on the mind of all of us. Listen to Dr. Blaser talk about it. Stay well and keep reading.

Job

Research Tech II – CHOP Microbiome Center

COVID-19

Editorial: Coronavirus: three things all governments and their science advisers must do now – Nature

World View: Don’t rush to deploy COVID-19 vaccines and drugs without sufficient safety guarantees – Shibo Jiang – Nature

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher & David Heymann – BMC Medicine

** Dr. Martin Blaser answers coronavirus questions from Twitter (full video available) – mlive.com

General microbiology

Regulation of fungal decomposition at single-cell level – Michiel Op De Beeck et al. – The ISME Journal

Antimicrobial resistance

** Broad-spectrum suppression of bacterial pneumonia by aminoglycoside-propagated Acinetobacter baumannii – M. Indriati Hood-Pishchany et al. – PLoS Pathogens

Vulnerability and resistance in the spatial heterogeneity of soil microbial communities under resource additions – Kelly Gravuer et al. – PNAS

Discovery of a novel integron-borne aminoglycoside resistance gene present in clinical pathogens by screening environmental bacterial communities – Maria-Elisabeth Böhm et al. – Microbiome

Characterization of antibiotic resistance and host-microbiome interactions in the human upper respiratory tract during influenza infection – Lingdi Zhang et al. – Microbiome

Human gut microbiome

The role of gut microbiota in bone homeostasis – Jyotirmaya Behera et al. – Bone

Animal experiments

Docosahexaenoate-enriched fish oil and medium chain triglycerides shape the feline plasma lipidome and synergistically decrease circulating gut microbiome-derived putrefactive postbiotics – Matthew I. Jackson & Dennis E. Jewell – PLoS One

Animal microbiome

The rodent vaginal microbiome across the estrous cycle and the effect of genital nerve electrical stimulation – Micah Levy et al. – PLoS One

The different dietary sugars modulate the composition of the gut microbiota in honeybee during overwintering – Hongfang Wang et al. – BMC Microbiology

Most dominant roles of insect gut bacteria: digestion, detoxification, or essential nutrient provision? – Tian-Zhong Jing et al. – Microbiome

Predictive ability of host genetics and rumen microbiome for subclinical ketosis – Grum Gebreyesus et al. – Journal of Dairy Science

Plant, root and soil microbiome

** Review: Agriculture and the Disruption of Plant–Microbial Symbiosis – Stephanie S. Porter & Joel L. Sachs – Trends in Ecology & Evolution

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil – Steven J. Blazewicz et al. – The ISME Journal

Reusing oil and gas produced water for agricultural irrigation: Effects on soil health and the soil microbiome – Hannah Miller et al. – Science of the Total Environment

Network analysis reveals the strengthening of microbial interaction in biological soil crust development in the Mu Us Sandy Land, northwestern China – Hong Zhou et al. – Soil Biology and Biochemistry

Water and extremophile microbiome

Performance and functional microbial communities of denitrification process of a novel MFC-granular sludge coupling system – Qiujin Deng et al. – Bioresource Technology

Microbial community structure and functional properties in permanently and seasonally flooded areas in Poyang Lake – Yang Liu et al. – Scientific Reports

Associations between redox-sensitive trace metals and microbial communities in a Proterozoic ocean analogue – Kathryn I. Rico et al. – Geobiology

Reactor configuration influences microbial community structure during high-rate, low-temperature anaerobic treatment of dairy wastewater – Paul G McAteer et al. – Bioresource Technology

Bioinformatics

Multiple-Disease Detection and Classification across Cohorts via Microbiome Search – Xiaoquan Su et al. – mSystems

Microbes in the news

How the mi­cro­biome is in­volved in the de­vel­op­ment of can­cer – Christian Urban – MedicalXpress

How a Fiber-Rich Plant-Based Diet Keeps Your Gut Microbiome Happy and Healthy – Chelsea Debret – One Green Planet

Gerhart: Keeping well during a pandemic – Timothy Gerhart – Your Valley

Study shows positive effect of cover crops on soil microbiome – AgriNews

Microbiome search engine can increase efficiency in disease detection and diagnosis – Chinese Academy of Sciences – EurekAlert

7 Ways A Gastroenterologist Supports His Microbiome & Overall Health – Marvin Singh – mbg Health

Infliximab Helps Gut Microbiome in Children with Crohn’s, Study Finds – Ana Pena – IBD News Today

Microbes on the market

DuPont, APC Microbiome Ireland link up for babies – Melody M. Bomgardner – C&EN

March 5, 2020

Today’s Digest is heavy, so you might want to pace yourself. It’s hard to pick the highlights, but I’m biased towards fungal research, so first about a wake-up call to look at the fungi seriously. The insects might provide for remedy against antibiotic resistance and is the dust settled on the sparse fetal intestinal microbiota? Stay healthy and keep reading.

Event

Call for papers – Global Outbreaks and Responses – BMC Medicine

General microbiology

** Viewpoints: Fungal diseases as neglected pathogens: A wake-up call to public health officials – Marcio L. Rodrigues & Joshua D. Nosanchuk – PLoS NTD

Inducible cell-to-cell signaling for tunable dynamics in microbial communities – Arianna Miano et al. – Nature Communications

Antimicrobial resistance

** The insect antimicrobial peptide cecropin A disrupts uropathogenic Escherichia coli biofilms – Miriam Kalsy et al. – npj Biofilms and Microbiomes

Using comparative genomics to understand molecular features of carbapenem-resistant Acinetobacter baumannii from South Korea causing invasive infections and their clinical implications – Min Hyung Kim – PLoS One

Factors associated with sufficient knowledge of antibiotics and antimicrobial resistance in the Japanese general population – Shinya Tsuzuki et al. – Scientific Reports

Faeces and vaccines could be the key to tackling antimicrobial resistance – Elisabeth Mahase – BMJ

A survey of extended-spectrum beta-lactamase-producing Enterobacteriaceae in urban wetlands in southwestern Nigeria as a step towards generating prevalence maps of antimicrobial resistance – Olawale Olufemi Adelowo et al. – PLoS One

Pregnancy and early life

** Viable bacterial colonization is highly limited in the human intestine in utero – E. Rackaityte et al. – Nature Medicine

Perinatal Antibiotic Exposure Affects the Transmission between Maternal and Neonatal Microbiota and Is Associated with Early-Onset Sepsis – Ping Zhou et al. – mSphere

Combined analysis of microbial metagenomic and metatranscriptomic sequencing data to assess in situ physiological conditions in the premature infant gut – Yonatan Sher et al. – PLoS One

Human skin microbiome

A microbiome and metabolomic signature of phases of cutaneous healing identified by profiling sequential acute wounds of human skin: An exploratory study – Mohammed Ashrafi et al. – PLoS One

Human oral microbiome

Review: Single-Cell Genomics and the Oral Microbiome – M. Balachandran et al. – Journal of Dental Research

Insights Obtained by Culturing Saccharibacteria With Their Bacterial Hosts – B. Bor et al. – Journal of Dental Research

Electronic Cigarette Aerosol Modulates the Oral Microbiome and Increases Risk of Infection – Smruti Pushalkar et al. – iScience

Press: Oral Microbiome Changes Implicated in Gum Inflammation in E-Cigarette Users – GenomeWeb

In vitro: A salivary metabolite signature that reflects gingival host-microbe interactions: instability predicts gingivitis susceptibility – Marcela M. Fernandez-Gutierrez et al. – Scientific Reports

Human respiratory microbiome

Review: The Role of Lung and Gut Microbiota in the Pathology of Asthma – Weronika Barcik et al. – Immunity

Cancer and microbiome

Endogenous murine microbiota member Faecalibaculum rodentium and its human homologue protect from intestinal tumour growth – Elena Zagato et al. – Nature Microbiology

Escherichia coli adhesion portion FimH functions as an adjuvant for cancer immunotherapy – Wei Zhang et al. – Nature Communications

Temporal changes in gut microbiota profile in children with acute lymphoblastic leukemia prior to commencement-, during-, and post-cessation of chemotherapy – Ling Ling Chua et al. – BMC Cancer

Review: Interplay between Dietary Polyphenols and Oral and Gut Microbiota in the Development of Colorectal Cancer – Carolina Cueva & Mariana Silva – Nutrients

Human gut microbiome

In vitro: Short-term supplementation of celecoxib-shifted butyrate production on a simulated model of the gut microbial ecosystem and ameliorated in vitro inflammation – Emma Hernandez-Sanabria et al. – npj Biofilms and Microbiomes

Review: Crosstalk Between Gut Microbiota and Innate Immunity and Its Implication in Autoimmune Diseases – Yuhao Jiao et al. – Frontiers in Immunology

An empirically derived method for measuring human gut microbiome alpha diversity: Demonstrated utility in predicting health-related outcomes among a human clinical sample – Sarah L. Hagerty et al. – PLoS One

Proof-of-concept study of the efficacy of a microbiota-directed complementary food formulation (MDCF) for treating moderate acute malnutrition – Ishita Mostafa et al. – BMC Public Health

Microbiota as Predictor of Mortality in Allogeneic Hematopoietic-Cell Transplantation – Jonathan U. Peled et al. – New England Journal of Medicine

Human multi-site microbiome

Age-Related Variation of Bacterial and Fungal Communities in Different Body Habitats across the Young, Elderly, and Centenarians in Sardinia – Lu Wu et al. – mSphere

Response of the human gut and saliva microbiome to urbanization in Cameroon – Ana Lokmer et al. – Scientific Reports

The gut-microbiota-brain axis

Therapeutic Effects of the In Vitro Cultured Human Gut Microbiota as Transplants on Altering Gut Microbiota and Improving Symptoms Associated with Autism Spectrum Disorder – Kainan Chen et al. – Microbial Ecology

Built environment microbiome

A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes – Anders B. Nygaard et al. – Scientific Reports

Metabolomics

Spatial metabolomics of in situ host–microbe interactions at the micrometre scale – Benedikt Geier et al. – Nature Microbiology

Global chemical effects of the microbiome include new bile-acid conjugations – Robert A. Quinn et al. – Nature

Animal experiments

PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice – Jingli Li et al. – Science of the Total Environment

Growth hormone deficiency and excess alter the gut microbiome in adult male mice – Elizabeth A Jensen et al. – Endocrinology

Dissociation of Adaptive Thermogenesis from Glucose Homeostasis in Microbiome-Deficient Mice – Tibor L. Krisko et al. – Cell Metabolism

Fecal IgA Levels Are Determined by Strain-Level Differences in Bacteroides ovatus and Are Modifiable by Gut Microbiota Manipulation – Chao Yang et al. – Cell Host & Microbe

Animal microbiome

Can rumen bacteria communicate to each other? – Mi-Young Won et al. – Microbiome

Entomopathogenic nematode-associated microbiota: from monoxenic paradigm to pathobiome – Jean-Claude Ogier et al. – Microbiome

The canine oral microbiome: variation in bacterial populations across different niches – Avika Ruparell et al. – BMC Microbiology

Evolutionary analysis of Mycobacterium bovis genotypes across Africa suggests co-evolution with livestock and humans – Osvaldo Frederico Inlamea et al. – PLoS NTD

Nanopore sequencing of microbial communities reveals the potential role of sea lice as a reservoir for fish pathogens – Ana Teresa Gonçalves et al. – Scientific Reports

Plant, root and soil microbiome

Insights on aquatic microbiome of the Indian Sundarbans mangrove areas – Paltu Kumar Dhal et al. – PLoS One

Ganoderma lucidum cultivation affect microbial community structure of soil, wood segments and tree roots – Fei Ren et al. – Scientific Reports

Effect of long-term destocking on soil fungal functional groups and interactions with plants – Jie Wang et al. – Plant and Soil

Comparative Analysis of Root Microbiomes of Rice Cultivars with High and Low Methane Emissions Reveals Differences in Abundance of Methanogenic Archaea and Putative Upstream Fermenters – Zachary Liechty et al. – mSystems

Fungal diversity and community composition of wheat rhizosphere and non-rhizosphere soils from three different agricultural production regions of South Africa – Magalane Pheladi Gqozo et al. – Applied Soil Ecology

Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat – Adam Ossowicki & Vittorio Tracanna et al. – Proceedings of the Royal Society B

Industrial development as a key factor explaining variances in soil and grass phyllosphere microbiomes in urban green spaces – Zhen-Zhen Yan et al. – Environmental Pollution

Plant communities mediate the interactive effects of invasion and drought on soil microbial communities – Catherine Fahey et al. – The ISME Journal

Water and extremophile microbiome

Methyl t-butyl ether-degrading bacteria for bioremediation and biocontrol purposes – Giada d’Errico et al. – PLoS One

Uncovering microbial responses to sharp geochemical gradients in a terrace contaminated by acid mine drainage – Rui Xu et al. – Environmental Pollution

Snapshot: Microbial Extremophiles – Amy K. Schmid et al. – Cell

Denitrification performance and microbial communities of solid-phase denitrifying reactors using poly (butylene succinate)/bamboo powder composite – Wanhe Qi et al. – Bioresource Technology

Meta-omics Provides Insights into the Impact of Hydrocarbon Contamination on Microbial Mat Functioning – Johanne Aubé et al. – Microbial Ecology

Role of microbial diversity for sustainable pyrite oxidation control in acid and metalliferous drainage prevention – Omy T. Ogbughalu et al. – Journal of Hazardous Materials

Phages and viruses

** Coronavirus research highlights – BMC

Fecal Viral Community Responses to High-Fat Diet in Mice – Anjelique Schulfer et al. – mSphere

Technology

Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens – Richard M. Leggett et al. – Nature Microbiology

Assembly-free single-molecule sequencing recovers complete virus genomes from natural microbial communities – John Beaulaurier et al. – Genome Research

Bioinformatics

Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing – Karel Břinda et al. – Nature Microbiology

Microbes in the news

Tough microbe’s DNA could be a lasting archive – Steve Nadis – Science

How Bacteria Can ‘Sculpt The Gut’ – Maya Trabulsi – KPBS

The bee microbiome can fight back against fungi that cause Colony Collapse Disorder – Lauren Sara McKee – Massive Science

Ancient gut microbiomes shed light on human evolution – Newswise

Launch of the Marine Microbiome Roadmap – NIOZ

Understanding Microbiome Resilience on a Changing Planet – Michigan State University

Adaptations in gut microbes helped our ancestors thrive in new geographical territories: Study – New Kerala

Scientists Announce VIRGO, First Comprehensive Gene Catalog To Decode the Vaginal Microbiome – PR Newswire

Metabolomics Reveals Connection Between Gut Microbiome and Blood – Metabolon

Study shows universally positive effect of cover crops on soil microbiome – Phys.org

New Center of Microbiome Science is in the works at Ohio State – Emily Caldwell – Ohio State University News

Common diseases may be communicable through microbiome, says UBC researcher – Stephanie Blain – The Ubyssey

The microbes in your mouth, and a reminder to floss and go to the dentist – Science Daily

For Your Microbiome, How You Eat Could Be As Important As What You Eat – Technology Networks

Study: Infectious gut bacteria may predict UTI risk – Sue Treiman – Cornell Chronicle

The Best Way to Avoid Getting Sick Is to Wash Your Hands — But You’re Probably Doing It Wrong – Bojana Galic – Live Strong

Microbes on the market

DuPont carries on microbiome momentum with metabolic disease collaboration – Will Chu – Nutraingredients

Non-microbiology picks

Invest 5% of research funds in ensuring data are reusable – Barend Mons – Nature