July 24, 2017

Here’s our Digest to start your Monday. The importance of managing the antibiotic resistance in perinatal and neonatal care, review on the plant-microbiota holobiont and poo bacteria found in three big fast food chains.

Jobs

Microbiology Lab Technician – Johnson County Community College – Overland Park, KS

Research Fellow – Microbiome Program Job – Mayo Clinic, Rochester MN

Pregnancy and infant microbiome

Book Chapter: Bacterial Infections in the Neonate – Morven S. Edwards & Carol J. Baker – Principles and Practice of Pediatric Infectious Diseases (Fifth Edition)

**Review: Antibiotic stewardship in perinatal and neonatal care Jayashree Ramasethu & Tetsuya Kawakita – Seminars in Fetal and Neonatal Medicine

Human liver microbiome

Sequencing the gut metagenome as a non-invasive diagnosis for advanced nonalcoholic steatohepatitis – Lixin Zhu et al. – Hepatology

Human gut microbiome

Comparative phenotypic analysis of “Clostridium neonatale” and Clostridium butyricum isolates from neonates – S. Schönherr-Helleca and G. Klein et al. – Anaerobe

The association of type II diabetes with gut microbiota composition – Fatemeh Navab-Moghadama et al. – Microbial Pathogenesis

The role of intestinal bacteria in the development and progression of gastrointestinal tract neoplasms – Kosuke Mima & Shuji Ogino et al. – Surgical Oncology

Review: The Microbiome in Crohn’s Disease : Role in Pathogenesis and Role of Microbiome Replacement Therapies – Sahil Khanna & Laura E. Raffals – Gastroenterology Clinics of North America

Review: The Gastric and Intestinal Microbiome: Role of Proton Pump Inhibitors – Artem Minalyan – Current Gastroenterology Reports

Animal experiments

The aerial parts of Salvia miltiorrhiza Bge. strengthen intestinal barrier and modulate gut microbiota imbalance in streptozocin-induced diabetic mice – Jun-Fei Gu et al. – Journal of Functional Foods

Intervention of probiotic L. reuteri fermented milk as an adjuvant to combat protein energy malnourishment induced gut disturbances in albino mice – S. Garg et al. – Journal of Functional Foods

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K. Jena et al. – The American Journal of Pathology

The title seems an overstatement: Microbial regulation of hippocampal miRNA expression: Implications for transcription of kynurenine pathway enzymes – Gerard M. Moloney et al. – Behavioural Brain Research

Helicobacter species are potent drivers of colonic T cell responses in homeostasis and inflammation – Jiani N. Chai et al. – Science Immunology

Press: How ‘Bad’ Gut Bacteria Can Change Their Evil Ways – Christopher Wanjek – LiveScience

Animal microbiome

Exploring a possible link between the intestinal microbiota and feed efficiency in pigs – Ursula M. McCormack et al. – Applied and Environmental Microbiology

Press: PIG MICROBIOME MAKEUP MAY INFLUENCE ANIMAL GROWTH RATE – Julie Wolf – ASM

Plant, root and soil microbiome

Review: Insights into plant phosphate sensing and signaling – Byung-Kook Ham et al. – Current Opinion in Biotechnology

Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars – Zhengkun Hu et al. – Soil Biology and Biochemistry

**Review: Understanding the holobiont: the interdependence of plants and their microbiome – Carmen Sánchez-Cañizares et al. – Current Opinion in Microbiology

Water and extremophile microbiome

Operation-driven heterogeneity and overlooked feed-associated populations in global anaerobic digester microbiome – Ran Mei et al. – Water Research

Preprint: Cytosine methylation within marine sediment microbial communities: potential epigenetic adaptation to the environment – Ian M. Rambo – bioRxiv

Phages and viruses

Bacteriophages in the human gut: our fellow travelers throughout life and potential biomarkers of heath or disease – Babak Bakhshinejad & Saeedeh Ghiasvand – Virus Research

Microbes in the news

Florida man contracts flesh-eating bacteria through blisters from hiking
Cherise Leclerc – WMUR9

Florida Seawater Bacteria Case Count Rises – Sherri Lonon – Patch

Shock as lab tests find of poo bacteria in products at McDonald’s, KFC and Burger King – Zara Whelan – Daily Post

Vaginal Probiotics Could Slow Zika & Other STD Infections – Sheryl Wood – Invisiverse

NASA Identifies What Kind of Fungi Could Grow in a Mars Habitat – Cynthia Wallentine – Invisiverse

July 21, 2017

Today’s digest is short and sweet. An interesting study of the microbial community composition inside the Internation Space Station using WGS. And, how a microbiologist is saving prairie dogs.

General Microbiome and Microbiology

Microbial metal resistance and metabolism across dynamic landscapes: high-throughput environmental microbiology

Carlson H.F1000Research

Animal and insect microbiome

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations

He X. Microbial Ecology

Plant, soil, and air microbiome

Metabarcoding: A powerful tool to investigate microbial communities and shape future plant protection strategies

Abdelfattah A.Biological Control

 Microbial functional diversity covaries with permafrost thaw‐induced environmental heterogeneity in tundra soil

Yuan MM.Global Change Biology

Marine and inland waters

Sulfide-Induced Dissimilatory Nitrate Reduction to Ammonium Supports Anaerobic Ammonium Oxidation (Anammox) in an Open-Water Unit Process Wetland

Jones ZL Applied and Environmental Microbiology

 The effects of phosphorus limitation on carbon metabolism in diatoms

Brembu T. Philosophical  Transaction of the Royal  Society B

Genetic and metabolic engineering in diatoms

Huang W. Philosophical  Transaction of the Royal  Society B

Built Microbiome

Microalgal hydrogen production-a review

Khetkorn W. Bioresource Technology

Whole metagenome profiles of particulates collected from the International Space Station

Nicholas AB.Microbiome, 2017

Microbes in the news

How a wildlife biologist became a plague-chaser in the American Southwest

STAT

July 19, 2017

Today’s digest is a long one! There is high diversity of studies, with a high abundance of gut microbiome studies, a few publications on fecal transplant, and some very interesting early life/pregnancy/mother-infant science.  A normal serving of animal studies, of course a nice colony of environmental microbial studies, and a study reporting the presence of bacteria in Alzheimer’s post-mortem brains.

Events and jobs

Postdoctoral research fellow in translational microbiome research – Department of Microbiology, Tumor and Cell Biology (MTC) at Karolinska Institutet

General microbiome

Commensal bacteria modulate the tumor microenvironment – Theofilos Poutahidis – Cancer Letters

[Review]  The human microbiome – Hubert E. Blum – Advances in Medical Sciences

Microbiome and Metabolome Data Integration Provides Insight Into Health and Disease – Michael Shaffer – Translational Research

Metabolic potential and taxonomic assessment of bacterial community of an environment to chronic industrial discharge – Neelam Devpura – International Biodeterioration & Biodegradation

Impact of the Microbiota on Bacterial Infections during Cancer Treatment – Jessica Galloway-Peña – Trends in Microbiology

Pregnancy and early life

** The Bacterial Ecosystem of Mother’s Milk and Infant’s Mouth and Gut – Elana Biagi – Frontiers in Microbiology | Evolutionary and Genomic Microbiology

* What’s Normal? Immune Profiling of Human Milk from Healthy Women Living in Different Geographical and Socioeconomic Settings – Lorena Ruiz – Frontiers in Immunology | Nutritional Immunology

Microbiome Associated with Severe Caries in Canadian First Nations Children – M. Agnello – Journal of Dental Research

* Bacterial communities found in placental tissues are associated with severe chorioamnionitis and adverse birth outcomes – Ronan M. Doyle – PLoS One

Human oral microbiome

Characterization of Oral Microbiota in Removable Dental Prosthesis Users: Influence of Arterial Hypertension – Leila Maria Marchi-Alves – BioMed Research International

Human vaginal microbiome

The association between ethnicity and vaginal microbiota composition in Amsterdam, the Netherlands – Hanneke Borgdorff – PLoS One

Human nearly-sterile sites

** 16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain – David C. Emery – Frontiers in Aging Neuroscience

Human gut microbiome

The Gut Microbiota of Healthy Chilean Subjects Reveals a High Abundance of the Phylum Verrucomicrobia – Sayaka Fujio-Vejar – Frontiers in Microbiology | Microbial Symbioses

*[Review] Significance of Microbiota in Obesity and Metabolic Diseases and the Modulatory Potential by Medicinal Plant and Food Ingredients – Hoda M. Eid – Frontiers in Pharmacology | Ethnopharmacology

MOLECULAR CHARACTERIZATION OF FECAL MICROBIOTA OF HEALTHY CHINESE TOBACCO SMOKER SUBJECTS IN SHAANXI PROVINCE, XI’AN CHINA – Ishaq HM – Journal of Ayub Medical College

The Microbiome in Posttraumatic Stress Disorder and Trauma-Exposed Controls: An Exploratory Study – Hemmings, Sian M.J – Psychosomatic Medicine

The Impact of Gut Microbiota on Gender-Specific Differences in Immunity – Floris Fransen – Frontiers in Immunology | Nutritional Immunology

Involvement of gut microbiota in the association between gastrointestinal motility and 5‑HT expression/M2 macrophage abundance in the gastrointestinal tract – Mo Yang – Molecular Medicine Reports

Correspondence: Fecal Microbiota Transplant from a Rational Stool Donor Improves Hepatic Encephalopathy: A Randomized Clinical Trial – Benjamin H Mullish – Hepatology

Going to the Bank: Fecal Microbiota Transplantation in Pediatrics – Elaine Barfield – Clinical Pediatrics

INTERRELATIONSHIPS BETWEEN GUT MICROBIOTA AND HOST: Paradigms, Role in Neurodegenerative Diseases and Future Prospects – Villarraso JC – CNS & Neurological Disorders Drug Targets

Faecal microbiota transplant: a novel biological approach to extensively drug-resistant organism-related non-relapse mortality – Innes AJ – Bone Marrow Transplantation

* Gut microbiota is critical for the induction of chemotherapy-induced pain – Shiqian Shen – Nature Neuroscience

Relationships between Gastrointestinal Microbiota and Blood Group Antigens – Anuhya Gampa – Physiological Genomics

[Masters Thesis] Evaluating the Effectiveness of Select Bacteria Against Clostridium difficile – Choquette, Kelsey Rose – Iowa State University, ProQuest Dissertations Publishing

* Potential and active functions in the gut microbiota of a healthy human cohort – Alessandro Tanca – Microbiome

[Letter to Editor] The necessity of gut microbiome characterization in diseases prevention and therapy – Sama Rezasoltani – Gastroenterology and Hepatology from Bed to Bench

[Review Article] The Intricate Interaction between Enteric Microbiota and Brain: Principles and Clinical Implications – Giovanni Gherardi – Journal of Digestive Diseases and Hepatology

Gut microbiota dysbiosis associated with glucose metabolism disorders and the metabolic syndrome in older adults – K Lippert – Beneficial Microbes

Animal experiments

Western Diet–Induced Dysbiosis in Farnesoid X Receptor Knockout Mice Causes Persistent Hepatic Inflammation after Antibiotic Treatment – Prasant K – The American Journal of Pathology

Grape pomace improves performance, antioxidant status, fecal microbiota and meat quality of piglets – I. Kafantaris – Animal

Animal microbiome

Microorganisms of the Intestinal Microbiota of Oncorhynchus Mykiss Produce Antagonistic Substances Against Bacteria Contaminating Food and Causing Disease in Humans – Lobos O – Italian Journal of Food Safety

Population-Specific Responses to Interspecific Competition in the Gut Microbiota of Two Atlantic Salmon (Salmo salar) Populations – Xiaoping He – Microbial Ecology

Habitat and indigenous gut microbes contribute to the plasticity of gut microbiome in oriental river prawn during rapid environmental change – Cheng-Yu Chen – PLoS One

Vertically and horizontally transmitted microbial symbionts shape the gut microbiota ontogenesis of a skin-mucus feeding discus fish progeny – François-Étienne Sylvain – Scientific Reports

Microbiome overview in swine lungs – Franciele Maboni Siqueira – PLoS One

Plant, root, and soil microbiome

Integrated metagenomics and molecular ecological network analysis of bacterial community composition during the phytoremediation of cadmium-contaminated soils by bioenergy crops – Zhaojin Chen – Ecotoxicology and Environmental Safety

Dynamics of Soil Bacterial Communities Over a Vegetation Season Relate to Both Soil Nutrient Status and Plant Growth Phenology – Davide Francioli – Microbial Ecology

Microbial Populations of Stony Meteorites: Substrate Controls on First Colonizers – Alastair W. Tait – Frontiers in Microbiology | Extreme Microbiology

Microbial functional diversity covaries with permafrost thaw-induced environmental heterogeneity in tundra soil – Mengting M. Yuan – Global Change Biology

[PrePrint] Conditionally rare taxa contribute but do not account for prokaryotic community changes in soils – Rachel Kaminsky – bioRxiv

Water and extremophile microbiome 

Performance and bacterial community structure of a 10-years old constructed mangrove wetland – Tingting Tian – Marine Pollution Bulletin

A comparative study revealed first insights into the diversity and metabolisms of the microbial communities in the sediments of Pacmanus and Desmos hydrothermal fields – Hai-liang Wang – PLoS One

Microbial Composition and Diversity Patterns in Deep Hyperthermal Aquifers from the Western Plain of Romania – Cecilia M. Chiriac – Microbiology of Aquatic Systems

Built environment

Pilot study to determine if microbial contamination levels in hospital washrooms are associated with hand drying method – Mark H. Wilcox – Journal of Hospital Infection

Probiotics / prebiotics

Arachidonic acid sex-dependently affects obesity through linking gut microbiota-driven inflammation to hypothalamus-adipose-liver axis – Pan Zhuang – BBA

Functional Characterization of Novel Faecalibacterium prausnitzii Strains Isolated from Healthy Volunteers: A Step Forward in the Use of F. prausnitzii as a Next-Generation Probiotic – Rebeca Martin – Frontiers in Microbiology | Food Microbiology

Bioinformatics

* Abundance estimation and differential testing on strain level in metagenomics data – Martina Fischer – Bioinformatics

Techniques

Development and Use of a Real-Time Quantitative PCR Method for Detecting and Quantifying Equol-Producing Bacteria in Human Faecal Samples and Slurry Cultures – Lucía Vázquez – Frontiers in Microbiology | Food Microbiology

Next-generation Sequencing of the DNA Virome from Fecal Samples – Monaco CL – Bio-protocol

Synthetic multispecies microbial communities reveals shifts in secondary metabolism and facilitates cryptic natural product discovery – Yutong Shi – Environmental Microbiology

Whole-genome sequencing of eukaryotes: From sequencing of DNA fragments to a genome assembly – K. S. Zadesenets – Russian Journal of Genetics

Microbes on the market

Microbiome Sequencing Services Market: trends, analysis, Overview, forecast up to 2021

Ed’s non-microbiology picks

Heavy metal accumulation by Saccharomyces cerevisiae cells armed with metal binding hexapeptides targeted to the inner face of the plasma membrane – Lavinia Liliana Ruta –Applied Microbiology and Biotechnology

Fracking can contaminate rivers and lakes with radioactive material, study finds

Subacute normobaric oxygen and hyperbaric oxygen therapy in drowning, reversal of brain volume loss: a case report – Paul G Harch – Medical Gas Research

No Effect of Commercial Cognitive Training on Neural Activity During Decision-Making – Joseph W. Kable – Journal of Neuroscience

Health Insurance Expansion and Incidence of Out‐of‐Hospital Cardiac Arrest: A Pilot Study in a US Metropolitan Community – Eric C. Stecker – Journal of the American Heart Association

July 18, 2017

A short Digest today, but with very interesting papers. Strain diversity implicated in atopic dermatitis, infant gut microbiome associated with cognitive development? And the sourdough microbiome.

General microbiology

Use of oxygen isotopes to differentiate between nitrous oxide produced by fungi or bacteria during denitrification – Lena Rohe et al. – Rapid Communications in Mass Spectrometry

Human skin microbiome

Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis – Allyson Byrd et al. – Science Translational Medicine

Human gut-microbiome-brain axis

Infant Gut Microbiome Associated with Cognitive Development – Alexander L. Carlson et al. – Biological Psychiatry

Press: In baby’s dirty diapers, the clues to baby’s brain development – UNC Health Care – EurekaAlert

Animal experiments

Peripartum Antibiotics Promote Gut Dysbiosis, Loss of Immune Tolerance, and Inflammatory Bowel Disease in Genetically Prone Offspring – Jun Miyoshi et al. – Cell Reports

Press: Higher IBD Risk in Offspring Associated With Antibiotic Use in Pregnancy – IDSE News Staff – IDSE

Microbes in the news

More Than Bread: Sourdough As a Window Into The Microbiome – Marcus Woo – NPR

Promising but take caution: Probiotics and Weight Loss – Philip J. Gregory – Medscape

Review article discusses potential role, benefits of non-rhizobia bacteria in root nodules of legume – Phys.org

Microbes on the market

Enterome, Nestlé Health Science Launch Microbiome Diagnostics Partners to Develop New IBD Treatments – Carolina Henriques – IBD News Today

Essential Science: Big investments for human microbiome research – Tim Sandle – Digital Journal

17, July 2017

In today’s digest, we learn more about how cloud-based computing is making it easier to analyses big datasets, and stochastic bottlenecks control bacterial colonization in animal host.

General Microbiome and Microbiology

New perspectives on dandruff and seborrheic dermatitis: lessons we learned from bacterial and fungal skin microbiota.

Paulino LC. European journal of dermatology

Harnessing microbiome‐based biotechnologies for sustainable mitigation of nitrous oxide emissions

Hu HW.Microbial Biotechnology

Human gut microbiome

Comparisons of Gut Microbiota Among Healthy Control, Patients With Conventional Adenoma, Sessile Serrated Adenoma, and Colorectal Cancer. Yoon H. Journal of Cancer Prevention

Genome-resolved metaproteomic characterization of preterm infant gut microbiota development reveals species-specific metabolic shifts and variabilities during early life. Xiong W. Microbiome

Assessing the impact of protein extraction methods for human gut metaproteomics

Zhang  X.Journal of Proteomics

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls

Stewart CJ. Microbiome

Animal and insect microbiome

Host–Microbe Interactions: Winning the Colonization Lottery

Lazzaro BP and GM Fox. Current Biology

Strategies for managing rival bacterial communities: lessons from burying beetles.

Kilner RM. Journal of Animal Ecology

Changes in the Gut Microbial Communities Following Addition of Walnuts to the Diet. Byerley, LO. Journal of Nutritional Biochemistry

Microbiome modelling

The Microbiome and Big Data

Navas-Molina JA. Current Opinion in Systems Biology

Plant, soil, and air microbiome

Differences in soil biological activity by terrain types at the sub-field scale in central Iowa US.

Kaleita AL.PloS one

Intercropping affects genetic potential for inorganic nitrogen cycling by root-associated microorganisms in Medicago sativa and Dactylis glomerata

Zhao M. Applied Soil Ecology

Changes in microbial community composition following phytostabilization of an extremely acidic Cu mine tailings

Yang T. Soil Biology and Biochemistry

Effects of between‐site variation in soil microbial communities and plant‐soil feedbacks on the productivity and composition of plant communities.   Bauer JT.Journal of Applied Ecology

Response of soil microbial communities to elevated antimony and arsenic contamination indicates the relationship between the innate microbiota and contaminant fractions. Sun W. Environmental Science and Technology

Marine and inland waters

The contribution of microbial biotechnology to mitigating coral reef degradation Damjanovic. Microbial Biotechnology

Metagenomic binning of a marine sponge microbiome reveals unity in defense but metabolic specialization

Slaby BM. The ISME Journal

Deep-Sea Hydrothermal Vent Viruses Compensate for Microbial Metabolism in Virus-Host Interactions

He T.  mBio

Built Microbiome

Microbial communities on painted wet and dry external surfaces of a historic fortress in Niterói, Brazil. Ogawa A. Journal of International Biodeterioration & Biodegradation

Preprint

Short reads from honey bee (Apis sp.) sequencing projects reflect microbial associate diversity.Gerth M.PeerJ

July 15, 2017

Enjoy your weekend with Saturdays microbiome digest. Lots of animal microbiome research out today, plus several human microbiome reviews and infant microbiome research.

Events and jobs

Molecular Scientist – Phage Display – Cambridge, UK

Research Officer Microbiology – Western Sydney, AUS

Research Assistant – Microbiology & Immunology – Illinois, USA

Medical Laboratory Scientist – Microbiology – Dunedin, New Zealand

General microbiome

Eco-Aging: stem cells and microbes are controlled by aging antagonist FoxO – Benedikt M Mortzfeld – Current Opinion in Microbiology

Gut–CNS-Axis as Possibility to Modulate Inflammatory Disease Activity—Implications for Multiple Sclerosis – Ann-Katrin Fleck – International Journal of Molecular Sciences

Pregnancy and early life

Early intervention with Bifidobacterium lactis NCC2818 modulates the host-microbe interface independent of the sustained changes induced by the neonatal environment – Marie C. Lewis – Scientific Reports

Virulence and Antibiotic Resistance of Enterococci Isolated from Healthy Breastfed Infants – Landete José M – Microbial Drug Resistance

Association of Antibiotics, Airway Microbiome and Inflammation in Infants with Cystic Fibrosis – Jessica E Pittman – Annals of the American Thoracic Society

Nasopharyngeal microbiota in infants and changes during viral upper respiratory tract infection and acute otitis media – Tasnee Chonmaitree – PLOS One

Human respiratory microbiome

A reproducible microcosm biofilm model of subgingival microbial communities – M. Fernandez y Mostajo – Journal of Periodontal Research

Review – Microbiome in chronic obstructive pulmonary disease – Eduard Monsó – Annals of Translational Medicine

Review – More than just a gut feeling: constraint-based genome-scale metabolic models for predicting functions of human intestinal microbes – Kees C. H – Microbiome

Review – The respiratory microbiome in idiopathic pulmonary fibrosis – Richard J. Hewitt – Annals of Translational Medicine

Human skin microbiome

Review – Cleanliness in context: reconciling hygiene with a modern microbial perspective – Roo Vandegrift – Microbiome

Human gut microbiome

High frequency of intestinal TH17 cells correlates with microbiota alterations and disease activity in multiple sclerosis – Ilaria Cosorich – Science Advances

Systematic review with meta-analysis: the efficacy of faecal microbiota transplantation for the treatment of recurrent and refractory Clostridium difficile infection – M. N. Quraishi – Alimentary Pharmacology & Therapeutics

Animal experiments 

Preprint – Disentangling metabolic functions of bacteria in the honey bee gut – Lucie Kesnerova – BioRxiv

Prion disease pathogenesis in the absence of the commensal microbiota – Barry M. Bradford – Journal of General Virology

A bidirectional association between the gut microbiota and CNS disease in a biphasic murine model of multiple sclerosis – Sara L. Colpitts – Gut Microbes

Effects of Consuming Xylitol on Gut Microbiota and Lipid Metabolism in Mice – Takashi Uebanso – Nutrients

Polydextrose changes the gut microbiome and attenuates fasting triglyceride and cholesterol levels in Western diet fed mice – Ghulam Shere Raza – Scientific Reports

Formula diet driven microbiota shifts tryptophan metabolism from serotonin to tryptamine in neonatal porcine colon – Manish Kumar Saraf – Microbiome

Regulation by gut bacteria of immune response, Bacillus thuringiensis susceptibility and hemolin expression in Plodia interpunctella – Alonso A.Orozco-Flores – Journal of Insect Physiology

Plant, root, and soil microbiome

Dynamics of culturable mesophilic bacterial communities of three fresh herbs and their production environment – Maria-Theresia Gekenidis – Journal of Applied Microbiology

Bioinformatics

Review – Insights into study design and statistical analyses in translational microbiome studies – Jyoti Shankar – Annals of Translational Medicine

Techniques

Assessing the impact of protein extraction methods for human gut metaproteomics – Xu Zhang – Journal of Proteomics

Microbes in the news

Micromotors are powered by bacteria, controlled by light  – Lisa Zyga – Phys.org

July 14, 2017

Events and jobs

Postdoc, Lieberman Lab

General microbiome

Assembly of Microbial Communities in Replicate Nutrient-Cycling Model Ecosystems Follows Divergent Trajectories, Leading to Alternate Stable States – Eulyn Pagaling – Environmental Microbiology

Human respiratory microbiome

Influence of lung CT changes in chronic obstructive pulmonary disease (COPD) on the human lung microbiome – Marion Engel – PLOS ONE

Human gut microbiome

Gut bacterial peptides with autoimmunity potential as environmental trigger for late onset complex diseases: In–silico study – Sapna Negi – PLOS ONE

Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study – Peggy S. Lai – PLOS ONE

Reduced Mass and Diversity of the Colonic Microbiome in Patients with Multiple Sclerosis and Their Improvement with Ketogenic Diet – Alexander Swidsinski – Frontiers in Microbiology

Longitudinal development of the gut microbiome and metabolome in preterm neonates with late onset sepsis and healthy controls – Christopher J. Stewart – Microbiome

Other Human microbiome

The oral bacterial microbiome of occlusal surfaces in children and its association with diet and caries – Apoena Aguiar Ribeiro – PLOS ONE

The oral fungal mycobiome: characteristics and relation to periodontitis in a pilot study – Brandilyn A. Peters – BMC Microbiology

Animal experiments

Three distinct pneumotypes characterize the microbiome of the lung in BALB/cJ mice – Julia Scheiermann – PLOS ONE

Assessment of gut microbiota populations in lean and obese Zucker rats – Reza Hakkak – PLOS ONE

Preparing the Gut with Antibiotics Enhances Gut Microbiota Reprogramming Efficiency by Promoting Xenomicrobiota Colonization – Shou K. Ji – Frontiers in Microbiology

Animal microbiome

On the core bacterial flora of Ixodes persulcatus (Taiga tick) – Shuo Sui – PLOS ONE

Skin microbiota in frogs from the Brazilian Atlantic Forest: Species, forest type, and potential against pathogens – Ananda Brito de Assis – PLOS ONE

Brackish habitat dictates cultivable Actinobacterial diversity from marine sponges – Gregory A. Ellis – PLOS ONE

Effects of Kluyveromyces marxianus supplementation on immune responses, intestinal structure and microbiota in broiler chickens – Weiwei Wang – PLOS ONE

Dominance-function relationships in the amphibian skin microbiome – Jenifer B. Walke – Environmental Microbiology

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis – J.N.Cullen – Veterinary Microbiology

Bacterial community composition in Adélie (Pygoscelis adeliae) and Chinstrap (Pygoscelis antarctica) Penguin stomach contents from Signy Island, South Orkney Islands – W. C. Yew – Polar Biology

Taxon abundance, diversity, co-occurrence and network analysis of the ruminal microbiota in response to dietary changes in dairy cows – Ilma Tapio – PLOS ONE

Honeybee (Apis mellifera)-associated bacterial community affected by American foulbrood: detection of Paenibacillus larvae via microbiome analysis – Tomas Erban – Scientific Reports

Plant, root, and soil microbiome

Shifts in the bacterial community composition along deep soil profiles in monospecific and mixed stands of Eucalyptus grandis and Acacia mangium – Arthur Prudêncio de Araujo Pereira – PLOS ONE

Maize Phyllosphere Microbial Community Niche Development Across Stages of Host Leaf Growth – Heather C. Manching – bioRxiv

Major phylum-level differences between porefluid and host rock bacterial communities in the terrestrial deep subsurface – Lily Momper – Environmental Microbiology Reports

Patterns of soil bacterial richness and composition tied to plant richness, soil nitrogen, and soil acidity in alpine tundra – Xia Yuan – Arctic, Antarctic, and Alpine Research

Water and extremophile microbiome

Unravelling riverine microbial communities under wastewater treatment plant effluent discharge in large urban areas – Yang Huo – Applied Microbiology and Biotechnology

Phages and viruses

Marine viruses discovered via metagenomics shed light on viral strategies throughout the oceans – Felipe H. Coutinho – Nature Communications

Science, publishing, and career

Jonathan Eisen named Faculty Director of the UC Davis Microbiome Initiative