September 26, 2019

Have a nice day! Today, in this digest we have a good number of papers, including those associated with beneficial microbes, compounds, and interventions. Some highlights: host-microbiome evolution, microbiome and urinary tract infections, the first reported bloodstream infection caused by gut-habiting Prevotella species, microbiome activity in halitosis, and more! Enjoy.   

 

General or Human Microbiome

The role of multilevel selection in host microbiome evolution – Simon van Vliet – PNAS

Review: Diagnosis of Urinary Tract Infection in the Neuropathic Bladder: Changing the Paradigm to Include the Microbiome – Catherine S. Forster – Topics in Spinal Cord Injury Rehabilitation 

Review: A critical review on diet-induced microbiota changes and cardiovascular diseases – Muthukumaran Jayachandran – Critical Reviews in Food Science and Nutrition 

Review: Microbiota: a novel regulator of pain – Manon Defaye – Journal of Neural Transmission

Relationship of tongue coating microbiome on volatile sulfur compounds in healthy and halitosis adults – Wei Ye – Journal of Breath Research

An Infectious Diseases Perspective on Fecal Microbiota Transplantation for Clostridioides difficile Infection in Children – Jillian M Cotter – Journal of the Pediatric Infectious Diseases Society

First bloodstream infection caused by Prevotella copri in a heart failure elderly patient with Prevotella-dominated gut microbiota: a case report – Patrizia Posteraro – Gut Pathogens

Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential – Ran Guo – British Journal of Anaesthesia

The Dysbiosis and Inter-Kingdom Synergy Model in Oropharyngeal Candidiasis, a New Perspective in Pathogenesis – Martinna Bertolini – Journal of Fungi

Microbiome Influence in the Pathogenesis of Prion and Alzheimer’s Diseases – Valeria D’Argenio – International Journal of Molecular Sciences

Protein Intake at Twice the RDA in Older Men Increases Circulatory Concentrations of the Microbiome Metabolite Trimethylamine-N-Oxide (TMAO) – Sarah M. Mitchell – Nutrients

Potential Strategies in the Prevention of Nonsteroidal Anti-inflammatory Drugs-Associated Adverse Effects in the Lower Gastrointestinal Tract – Chuan-Guo Guo – Gut and Liver

 

Composition of gut microbiota of children and adolescents with perinatal HIV infection taking antiretroviral therapy in Zimbabwe – Trym T Flygel – The Journal of Infectious Diseases

Gut Microbiome in Psoriasis is Perturbed Differently During Secukinumab and Ustekinumab Therapy and Associated with Response to Treatment – Nai-Lun Yeh – Clinical Drug Investigation

The association between gut microbiota development and maturation of intestinal bile acid metabolism in the first 3 y of healthy Japanese infants – Masaru Tanaka – Gut Microbes

 

Animal Microbiome

Food Preservatives Induce Proteobacteria Dysbiosis in Human-Microbiota Associated Nod2-Deficient Mice – Lucia Hrncirova – Microorganisms

Maternal Dietary Protein Intake Influences Milk and Offspring Gut Microbial Diversity in a Rat (Rattus norvegicus) Model –  Matthew F. Warren – Nutrients

Microbiota, Gut Health and Chicken Productivity: What Is the Connection? – Juan M. Diaz Carrasco – Microorganisms

Microbiota Composition and Functional Profiling Throughout the Gastrointestinal Tract of Commercial Weaning Piglets – Raphaële Gresse – Microorganisms 

Microbiota fingerprints within the oral cavity of cetaceans as indicators for population biomonitoring – Pedro Soares-Castro – Scientific Reports

Core gut microbial communities are maintained by beneficial interactions and strain variability in fish – Fotini Kokou – Nature Microbiology

Beneficial Microbes and Compounds

Role of Dietary Flavonoid Compounds in Driving Patterns of Microbial Community Assembly – Kerry L. Ivey – mBio

Oral Administration of β-Glucan and Lactobacillus plantarum Alleviates Atopic Dermatitis-like Symptoms – In Sung Kim – Journal of Microbiology and Biotechnology

Protective Effect of Probiotic Bacteria and Estrogen in Preventing HIV-1-Mediated Impairment of Epithelial Barrier Integrity in Female Genital Tract – Sara Dizzell – Cells (MPDI)

Fish Oil, but Not Olive Oil, Ameliorates Depressive-Like Behavior and Gut Microbiota Dysbiosis in Rats under Chronic Mild Stress – Te-Hsuan Tung – Biomolecules

The Potential Impact of Probiotics on the Gut Microbiome of Athletes – Laura Wosinska – Nutrients

Royal Jelly and Its Components Promote Healthy Aging and Longevity: From Animal Models to Humans – Hiroshi Kunugi – International Journal of Molecular Sciences

Postbiotics and Their Potential Applications in Early Life Nutrition and Beyond – Carrie A. M. Wegh – International Journal of Molecular Sciences

Antifungal and Antivirulence Activity of Vaginal Lactobacillus Spp. Products against Candida Vaginal Isolates – Camilla Itapary dos Santos – Pathogens

Metabolic and Vascular Effect of the Mediterranean Diet – Antonino Tuttolomondo – International Journal of Molecular Sciences

 

Environmental Microbiome

Unveiling resistome profiles in the sediments of an Antarctic volcanic island – V.B. Centurion – Environmental Pollution

Functional metagenomic analysis of dust-associated microbiomes above the Red Sea – Nojood A. Aalismail – Scientific Reports

 

Bioinformatics

The EFI Web Resource for Genomic Enzymology Web Tools: Leveraging Protein, Genome, and Metagenome Databases to Discover Novel Enzymes and Metabolic Pathways – Rémi Zallot – Biochemistry

Pavian: Interactive analysis of metagenomics data for microbiome studies and pathogen identification – Florian P Breitwieser – Biochemistry

 

Methods

Review: Common principles and best practices for engineering microbiomes – Christopher E. Lawson – Nature Reviews Microbiology

Sample Preservation and Storage Significantly Impact Taxonomic and Functional Profiles in Metaproteomics Studies of the Human Gut Microbiome – Oskar Hickl – Microorganisms

Optimizing bacterial DNA extraction in urine – Matthew M. Munch – PLoS One

 

September 23, 2019

This Monday, check out the largest ever study of neonatal microbiomes, the study where researchers alter mouse gut microbiomes by feeding good bacteria their preferred fibers, and the study about the significant effect of antibiotics, antivirals and cofactors on the gut microbiome. Happy reading!

Pregnancy and early life

*Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth – Yan Shao – Nature

Gut microbiome

*Interspecies Competition Impacts Targeted Manipulation of Human Gut Bacteria by Fiber-Derived Glycans – Michael Patnode – Cell

*Distinct impact of antibiotics on the gut microbiome and resistome: a longitudinal multicenter cohort study – Matthias Willmann – BMC Biology

Identification of gut microbiome markers for schizophrenia delineates a potential role of Streptococcus – Feng Zhu – bioRxiv

Fecal Microbiotas of Indonesian and New Zealand Children Differ in Complexity and Bifidobacterial Taxa during the First Year of Life – Blair Lawley – Applied and Environmental Microbiology

Light-entrained and brain-tuned circadian circuits regulate ILC3s and gut homeostasis – Cristina Godinho-Silva – Nature

Baseline human gut microbiota profile in healthy people and standard reporting template – Charles H. King – PlosOne

Oral microbiome

Taste perception and oral microbiota are associated with obesity in children and adolescents – Chiara Mameli – PlosOne

Urinary microbiome

The urobiome of continent adult women: a cross-sectional study – Travis Price – Obstetrics & Gynaecology

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota – Fei Li – bioRxiv

Respiratory microbiome

The effects of e-cigarette vapor exposure on the transcriptome and virulence of Streptococcus pneumoniae – Kamal Bagale – bioRxiv

Water microbiome

Diversity patterns of marine heterotrophic culturable bacteria along vertical and latitudinal gradients – Isabel Sanz-Sáez – bioRxiv

Laundry wastewater and domestic sewage pilot-scale anaerobic treatment: Microbial community resilience regarding sulfide production – A.G.L. Moura – Journal of Environmental Management

Distinct responses from bacterial, archaeal and fungal streambed communities to severe hydrological disturbances – G. Gionchetta – Scientific reports

Metagenome of a polluted river reveals a reservoir of metabolic and antibiotic resistance genes – Parul Mittal – Environmental Microbiome

Plant/root/soil microbiome

Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome – Xiaoxuan Guo – Plant Communications

Metatranscriptomics reveals climate change effects on the rhizosphere microbiomes in European grassland – Qicheng Bei – Soil Biology and Biochemistry

Phages and viruses

Beyond cells – The virome in the human holobiont – Rodrigo García-López – Microbial cells

ViraMiner: Deep learning on raw DNA sequences for identifying viral genomes in human samples – Ardi Tampu – PlosOne

Bioinformatics

Review: The signal and the noise – characteristics of antisense RNA in complex microbial communities – Thomas Yssing Michaelsen – bioRxiv

SuRF: a New Method for Sparse Variable Selection, with Application in Microbiome Data Analysis – Lihui Liu – arXiv

September 13, 2019

In today’s edition, you’ll find a whole new textbook about microbes affecting ecosystem sustainability, reviews about phages and plant viruses, New York Times coverage of clinical trials of FMT for obesity, how to banish “manels” from scientific meetings, and microbiota-related metabolites as biomarkers of aging. Enjoy!

General microbiome
Review: Microbial invasions in terrestrial ecosystems – Madhav P. Thakur – Nature Reviews Microbiology

Preprint: Therapeutically exploring persister metabolism in bacteria – Sayed G. Mohiuddin – bioRxiv

Preprint: Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations – Kelsey M Hallinen – bioRxiv

Human gut microbiome
Review: Pairing phages with their hosts in the human gut – Ursula Hofer – Nature Reviews Microbiology

Book chapter: Gut Microbiota and Microbiota-Related Metabolites as Possible Biomarkers of Cognitive Aging – Andrea Ticinesi – Reviews on Biomarker Studies in Aging and Anti-Aging Research

Animal microbiome
Habitat disturbance and the organization of bacterial communities in Neotropical hematophagous arthropods – Kelly L. Bennett – PLOS One

Plant, root, soil microbiome
Book chapter: Rhizospheric Microbiome Engineering as a Sustainable Tool in Agriculture: Approaches and Challenges – Shubham Dubey – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Dynamics of Plant Microbiome and Its Effect on the Plant Traits – Shivali Sharma – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Book chapter: Microbial Diversity of the Sundarbans, the World’s Largest Tidal Mangrove Forest, and Its Bioprospects – Kaushik Biswas – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

Water and extremophile microbiome
Capability for arsenic mobilization in groundwater is distributed across broad phylogenetic lineages – Robert E. Danczak – PLOS One

Food microbiology
Book chapter: Microbial Diversity on Grapes and Other Fruits: Role and Significance in Fermentation – M. V. Deshpande – Microbial Diversity in Ecosystem Sustainability and Biotechnological Applications

The Dynamics Analysis of Fungal Community Diversity During the Fermentation Process of Chinese Traditional Soybean Paste – Jingping Ge – Waste and Biomass Valorization

Phages and viruses
Review: Evolution and ecology of plant viruses – Pierre Lefeuvre – Nature Reviews Microbiology

Bioinformatics
An Integrated Approach for Efficient Multi-Omics Joint Analysis – Massimiliano S. Tagliamonte – Proceedings of the 10th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics

Techniques
Polysaccharide-based liquid storage and transport media for non-refrigerated preservation of bacterial pathogens – Janine R. Hutchison – PLOS One

Microbes in the news
Seeking an Obesity Cure, Researchers Turn to the Gut Microbiome -Anahad O’Connor – NY Times

Exclusive: Behind the front lines of the Ebola wars – Amy Maxmen – Nature

Science, publishing, and career
How to banish manels and manferences from scientific meetings – Holly Else – Nature

September 3, 2019

Happy Tuesday and best of luck to those headed back to school! In today’s Digest, you’ll find the virome of the mosquito gut, leveraging blood metabolomics to predict gut alpha diversity, and a comparison of bacterial taxa consumed in organic vs. conventional apples.

General microbiome
Changes in microbial community structure during dark fermentative hydrogen production – Guang Yang – International Journal of Hydrogen Energy

Pregnancy and early life
Effect of the vaginal microbiome on the pregnancy rate in women receiving assisted reproductive treatment – Andrea Bernabeu – Journal of Assisted Reproduction and Genetics

Maturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease – Nicholas Rhoades – Genome Biology

Human gut microbiome
Blood metabolome predicts gut microbiome α-diversity in humans – Nature Biotechnology – Tomasz Wilmanski

B cell superantigens in the human intestinal microbiota – Jeffrey J. Bunker – Science Translational Medicine

Long-read metagenomic exploration of extrachromosomal mobile genetic elements in the human gut – Yoshihiko Suzuki – Microbiome

Microbiome of death
Preprint: Manner of death and demographic effects on microbial community composition in organs of the human cadaver – Holly L Lutz – bioRxiv

Animal experiments
Diet-induced remission in chronic enteropathy is associated with altered microbial community structure and synthesis of secondary bile acids – Shuai Wang – Microbiome

Animal microbiome
Testing the relationship between microbiome composition and flux of carbon and nutrients in Caribbean coral reef sponges – Shelby E. Gantt – Microbiome

Plant, root, and soil microbiome
A new family of uncultivated bacteria involved in methanogenesis from the ubiquitous osmolyte glycine betaine in coastal saltmarsh sediments – Helen J. Jones – Microbiome

Top-down Enrichment Guides in Formation of Synthetic Microbial Consortia for Biomass Degradation – Sean P. Gilmore – ACS Synthetic Biology

Microbial community response to environmental changes in a technosol historically contaminated by the burning of chemical ammunitions – Hugues Thouin – Science of the Total Environment

Preprint: Intra-genus metabolic diversity facilitates co-occurrence of multiple Ferrovum species at an acid mine drainage site – Christen L Grettenberger – bioRxiv

Water and extremophile microbiome
Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics – Yulin Wang – Microbiome

Fungi in salterns – Dawoon Chung – Journal of Microbiology

Distinct temporal dynamics of planktonic archaeal and bacterial assemblages in the bays of the Yellow Sea – Jong-Geol Kim – Plos One

Food microbiology
An Apple a Day: Which Bacteria Do We Eat With Organic and Conventional Apples? – Birgit Wassermann – Frontiers in Microbiology

Preprint: Molecular characterization of bacterial communities in sheep cheese through 16S rRNA gene sequencing – Creciana Maria Endres – bioRxiv

Phages and viruses
Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics – Chenyan Shi – Microbiome

The virome of cerebrospinal fluid: viruses where we once thought there were none – Chandrabali Ghose – Frontiers in Microbiology

Detecting viral sequences in NGS data – Paul G. Cantalupo – Current Opinion in Virology

Bioinformatics
Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm – Suraj Gupta – Microbiome

August 15, 2019

Have a nice Thursday! Today we have a set of papers showing randomized trials related to antibiotic use and alimentary interventions, metabolic networks associated with C. difficile infection, and analysis of E. coli isolates from human stool. Today, we also include a couple of protocol papers about the use of stable isotope probing in plant microbiome research.

 

Human and General Microbiome

Gut microbiome alteration in MORDOR I: a community-randomized trial of mass azithromycin distribution – T. Doan – Nature Medicine 

Fecal microbiome and metabolome of infants fed bovine MFGM supplemented formula or standard formula with breast-fed infants as reference: a randomized controlled trial – Xuan He – Scientific Reports

Antibiotic Resistance, Virulence Factors, Phenotyping, and Genotyping of E. coli Isolated from the Feces of Healthy Subjects – Stefano Raimondi – Microorganisms

Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections – John I. Robinson – The Journal of Clinical Investigation

Antibiotic exposure and ‘response failure’ for subsequent respiratory tract infections: an observational cohort study of UK preschool children in primary care – Oliver van Hecke – British Journal of General Practice 

Abnormal vaginal microbiome associated with vaginal mesh complications – Nikolaus Veit‐Rubin – Neurology and Urodynamics

Acceptability, Tolerability and Safety of Faecal Microbiota Transplantation in patients with active Ulcerative Colitis (AT&S Study) – Ajit Sood – Journal of Gastroenterology and Hepatology

The bacteriome of otitis media with effusion: Does it originate from the adenoid? – Oguz Ari – International Journal of Pediatric Otorhinolaryngology 

An Exploratory Analysis of Fecal Immunochemical Test Performance for Colorectal Cancer Screening in Nigeria – Gregory C. Knapp – World Journal of Surgery

Isolates from colonic spirochaetosis in humans show high genomic divergence and potential pathogenic features but are not detected using standard primers for the human microbiota – Kaisa Thorell – Journal of Bacteriology

Microbiota-derived Trimethylamine N-oxide Predicts Cardiovascular Risk After STEMI – Yasushi Matsuzawa – Scientific Reports

Review: Targeting Microbiota: What Do We Know about It at Present? – Aleksejs Derovs – Medicina

Tech News: Reproducibility: the search for microbiome standards – Joseph Martin – BioTechniques

 

Animal Microbiome

Intestinal microbial products from alcohol-fed mice contribute to intestinal permeability and peripheral immune activation – Derrick R. Samuelson – Alcoholism

Comparative metagenomic sequencing analysis of cecum microbiotal diversity and function in broilers and layers – Zhao Qi – 3 Biotech

Oligosaccharides Modulate Rotavirus-Associated Dysbiosis and TLR Gene Expression in Neonatal Rats – Ignasi Azagra-Boronat – Cells

Role of coprophagy in the cecal microbiome development of an herbivorous bird Japanese rock ptarmigan – Atsushi Kobayashi – Journal of Veterinary Medical Science

 

Beneficial compounds and microbes

Review: The role of gut microbiota for the activity of medicinal plants traditionally used in the European Union for gastrointestinal disorders – Timo A. Thumann – Journal of Ethnopharmacology

Commentary: Microbiome, probiotics and dermatology – J.A. Cardenas‐de la Garza – British Journal of Dermatology

Cooked Red Lentils Dose-Dependently Modulate the Colonic Microenvironment in Healthy C57Bl/6 Male Mice – Daniela Graf – Nutrients

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study – Kensei Nishida – Nutrients 

Effect of coffee on the compositional shift of oral indigenous microbiota cultured in vitro – 

 

Food Microbiome

Microbial Transformations of Organically Fermented Foods – Ruma Raghuvanshi – Metabolites

 

Plant Microbiome

Protocol: Stable Isotope Probing of Microbiota Structure and Function in the Plant Rhizosphere – Wafa Achouak – Stable Isotope Probing (Methods in Molecular Biology)

Protocol: Targeted Metatranscriptomics of Soil Microbial Communities with Stable Isotope Probing – Ang Hu – Stable Isotope Probing (Methods in Molecular Biology)

Environmental pollution effects on plant microbiota: the case study of poplar bacterial-fungal response to silver nanoparticles – Francesco Vitali – Applied Microbiology and Biotechnology

May 4, 2019

Have a good weekend! Today, in this MB, we have interesting papers about different aspects of the microbiome. For example, we have a review overviewing the relationship between epigenetic changes, microbiome and metabolic diseases, as well as a paper focused in the use of a microbial metabolite in the prognosis of coronary issues. We have also the publication of an interesting study authored by the MB founder Elisabeth Bik.

There are also some papers about coral microbiome and an study about the homogenization of the microbiome between both US Air Force cadets and their built environment.

 

Human and General Microbiome

Review: Epigenetic Markers and Microbiota/Metabolite-Induced Epigenetic Modifications in the Pathogenesis of Obesity, Metabolic Syndrome, Type 2 Diabetes, and Non-alcoholic Fatty Liver Disease – Daniela Stols-Gonçalves – Current Diabetes Reports

A novel sequencing-based vaginal health assay combining self-sampling, HPV detection and genotyping, STI detection, and vaginal microbiome analysis – Elisabeth Bik – PLoS ONE

Trimethyllysine, a trimethylamine N-oxide precursor, provides near- and long-term prognostic value in patients presenting with acute coronary syndromes – Xinmin S Li – European Heart Journal

Review: The interaction between Entamoeba histolytica and enterobacteria shed light on an ancient antibacterial response – Nancy Guillén – Cellular Microbiology

PCR Characterization of Microbiota on Contracted and Non-Contracted Breast Capsules – Yara Bachour – Aesthetic Plastic Surgery

Decreased Cephalosporin Susceptibility of Oropharyngeal Neisseria Species in Antibiotic-Using Men-who-have-sex-with-men of Hanoi, Vietnam– Huan V Dong – Clinical Infectious Diseases

Review: Smoking and periodontal microorganisms – Takashi Hanioka – Japanese Dental Science Review

The influence of the vaginal microbiota on preterm birth: A systematic review and recommendations for a minimum dataset for future research – Myrthe JCS. Peelen – Placenta

Gut Microbiome in Health and Disease: Emerging Diagnostic Opportunities – Aonghus Lavelle – Gastroenterology Clinics of North America

Laryngotracheal Microbiota in Adult Laryngotracheal Stenosis – Alexander T. Hillel – mSphere

Antibiotic Resistance Gene Diversity and Virulence Gene Diversity Are Correlated in Human Gut and Environmental Microbiomes – Pedro Escudeiro –  mSphere

 

Beneficial Microbes

Review: Changing our microbiome: Probiotics in dermatology – Y. Yu – British Journal of Dermatology

Amelioration of obesity-related biomarkers by Lactobacillus sakei CJLS03 in a high-fat diet-induced obese murine model – Josep Ji – Scientific Reports

 

Animal Models / Animal Microbiome

Age-related analysis of the gut microbiome in a purebred dog colony – Keijiro Mizukami – FEMS Microbiology Letters

Addition of plant dietary fibre to a raw red meat high protein, high fat diet, alters the faecal bacteriome and organic acid profiles of the domestic cat (Felis catus) – Christina F. Butowski – PLoS ONE

Effects of diet on gut microbiota of soil collembolans – Qian Xiang – Science of The Total Environment

Multiple stressors interact primarily through antagonism to drive changes in the coral microbiome – Rebecca L. Maher – Scientific Reports

Structure and stability of the coral microbiome in space and time – Courtney M. Dunphy – Scientific Reports

The effect of dissolved nickel and copper on the adult coral Acropora muricata and its microbiome – Francesca Gissi – Environmental Pollution

 

Food Microbiome

Microbiota and Chemical Compounds in Fermented Pinelliae Rhizoma (Banxiaqu) from Different Areas in the Sichuan Province, China – Bo Shu – Polish Journal of Microbiology

 

Built Environment

Longitudinal homogenization of the microbiome between both occupants and the built environment in a cohort of United States Air Force Cadets –  Anukriti Sharma – Microbiome

 

Environmental Microbiome

The Influence of Temperature and Nitrogen Source on Cellulolytic Potential of Microbiota Isolated from Natural Environment –  Agnieszka Wita  – Polish Journal of Microbiology

 

Techniques

The potential of nanoflow liquid chromatography-nano electrospray ionisation-mass spectrometry for global profiling the faecal metabolome – Andrew J. Chetwynd – Journal of Chromatography A

8 April, 2019

General Microbiome

Coevolutionary dynamics shape the structure of bacteria-phage infection networks. Fortuna MA.Evolution.

High proportions of bacteria are culturable across major biomes. Martiny AC. ISME Journal

The complexity of an optimal vaginal biome. Eschenbach DA. BJOG

The lung microbiome, vitamin D, and the tuberculous granuloma: A balance triangle. Balcells ME. Microbial Pathogenesis

Gut Microbiome

The parasitic worm product ES-62 normalises the gut microbiota bone marrow axis in inflammatory arthritis. Doonan J. Nature Communications

Culture-enriched human gut microbiomes reveal core and accessory resistance genes. Raymond F.Microbiome.

Plant, Soil, Water, and Air Microbiome

Temperature and soil moisture control microbial community composition in an arctic-alpine ecosystem along elevational and micro-topographic gradients.Frindte K. ISME Journal

Root traits and belowground herbivores relate to plant-soil feedback variation among congeners.Wilschut RA. Nature Communications

A Polyphasic Approach for Assessing Eco-System Connectivity Demonstrates that Perturbation Remodels Network Architecture in Soil Microcosms.Stamou GP. Microbial Ecology

Effect of stock density on the microbial community in biofloc water and Pacific white shrimp (Litopenaeus vannamei) gut microbiota.Deng Y. Applied Microbiology Biotechnology

Rapid and stable microbial community assembly in the headwaters of third-order stream. Teachey ME. Applied Environmental Microbiology

Comparative Metagenomics Reveals Enhanced Nutrient Cycling Potential After Two Years of Biochar Amendment in a Tropical Oxisol. Yu J. Applied Environmental Microbiology

Animal Experiments and Microbiome

Effect of a low protein diet on chicken ceca microbiome and productive performances. De Cesare A. Poultry Science

Impact of a probiotic-based cleaning product on the microbiological profile of broiler litters and chicken caeca microbiota.De Cesare P. Poultry Science

Metagenomic Analysis of the Whole Gut Microbiota in Brazilian Termitidae Termites Cornitermes cumulans, Cyrilliotermes strictinasus, Syntermes dirus, Nasutitermes jaraguae, Nasutitermes aquilinus, Grigiotermes bequaerti, and Orthognathotermes mirim. Grieco MB. Current Microbiology.

The hemolymph microbiome of insects. Blow F. Journal Of Insect Physiology

Musa basjoo regulates the gut microbiota in mice by rebalancing the abundance of probiotic and pathogen. Wei T. Microbial Pathogenesis

Investigating the influence of organic acid marinades, storage temperature and time on the survival/inactivation interface of Salmonella on chicken breast fillets.

Lytou AE. International Journal of Food Microbiology.