July 5, 2020

Pregnancy and early life
Natural environments in the urban context and gut microbiota in infants – Neilsen et al. – Environment International

Human nearly-sterile sites
Breast cancer colonization by Fusobacterium nucleatum accelerates tumor growth and metastatic progression – Parhi et al. – Nature Communications

Enrichment of the airway microbiome in people living with HIV with potential pathogenic bacteria despite antiretroviral therapy – Rofael et al. – EClinicalMedicine

Human microbiome in vitro and ex vivo experiments
Triclosan has a robust, yet reversible impact on human gut microbial composition in vitro – Mahalak et al. – PLOS One

Animal experiments
Alterations of gut microbiota and serum bile acids are associated with parenteral nutrition-associated liver disease – Wang et al. – Journal of Pediatric Surgery

Colonic microbiome profiles for improved feed efficiency can be identified despite major effects of farm of origin and contemporary group in pigs – Vigors et al. – Animal

Gut microbiota profiles of commercial laying hens infected with tumorigenic viruses – Wan et al. – BMC Veterinary Research

Alterations of gut microbiota contribute to the progression of unruptured intracranial aneurysms – Li et al. – Nature Communications

Animal microbiome
Review: The Effects of Nutrition on the Gastrointestinal Microbiome of Cats and Dogs: Impact on Health and Disease – Wernimont et al. – Frontiers in Microbiology

Individual and Site-Specific Variation in a Biogeographical Profile of the Coyote Gastrointestinal Microbiota – Sugden et al. – Microbial Ecology

Assessment of bacterial diversity of Rhipicephalus microplus ticks from two livestock agroecosystems in Antioquia, Colombia – Segura et al. – PLOS One

Microbiome diversity in Diaphorina citri populations from Kenya and Tanzania shows links to China – Ajene et al. – PLOS One

Plant, root, and soil microbiome
Metagenomics analysis of fungal communities associated with postharvest diseases in pear fruits under the effect of management practices – Zambounis et al. – Archives of Microbiology

Water and extremophile microbiome
The Efficacy of Hydrogen Peroxide in Mitigating Cyanobacterial Blooms and Altering Microbial Communities across Four Lakes in NY, USA – Lusty and Gobler – Toxins

Seasonal effects of river flow on microbial community coalescence and diversity in a riverine network – Luo et al. – FEMS Microbiology Ecology

Microbial community composition across a coastal hydrological system affected by submarine groundwater discharge (SGD) – Adyasari et al. – PLOS One

The contribution of microbial communities in polymetallic nodulesto the diversity of the deep-sea microbiome of the Peru Basin(4130–4198 m depth) – Molari et al. – Biogeosciences

Probiotics / prebiotics
Review: Toward a systematic design of smart probiotics – Choudhary and Mahadevan – Current Opinion in Biotechnology

A Novel Non-Digestible, Carrot-Derived Polysaccharide (cRG-I) Selectively Modulates the Human Gut Microbiota while Promoting Gut Barrier Integrity: An Integrated In Vitro Approach – Van den Abbeele et al. – Nutrients

Bioinformatics
Review: What Is Metagenomics Teaching Us, and What Is Missed? – New and Brito – Annual Review of Microbiology

July 4, 2020

Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al.,Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al.,Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasisChuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al.,Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al.,Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al,Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al.,New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al.,Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al.,Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al.,BioRxiv

July 3rd, 2020

General microbiome

Microbiome definition re-visited: old concepts and new challenges – Berg et al. Microbiome

Large-scale metabolic interaction network of the mouse and human gut microbiota. – Lim et al. Scientific Data

Early life microbiome

Very early-life exposure to microbiota-induced TNF drives the maturation of neonatal pre-cDC1 – Kohler et al. Gut.

Human gut microbiome

Arrhythmic Gut Microbiome Signatures Predict Risk of Type 2 Diabetes – Reitmeier et al. Cell Host & Microbe

Ranking microbiome variance in inflammatory bowel disease: a large longitudinal intercontinental study – Clooney et al. Gut

Cholesterol Metabolism by Uncultured Human Gut Bacteria Influences Host Cholesterol Level – Kenny et al. Cell Host & Microbe

Amending microbiota by targeting intestinal inflammation with TNF blockade attenuates development of colorectal cancer – Yang et al. Nature Cancer

Animal microbiome

A Systematic Analysis of Mosquito-Microbiome Biosynthetic Gene Clusters Reveals Antimalarial Siderophores that Reduce Mosquito Reproduction Capacity – Ganley et al. Cell Chemical Biology

Extremophile microbiome

Microbial succession during the transition from active to inactive stages of deep-sea hydrothermal vent sulfide chimneys – Hou et al. BMC Microbiome

Phages and viruses

Phase-variable capsular polysaccharides and lipoproteins modify bacteriophage susceptibility in Bacteroides thetaiotaomicron – Porter et al. Nature Microbiology

Bioinformatics

ATLAS: a Snakemake workflow for assembly, annotation, and genomic binning of metagenome sequence data – Kieser et al. BMC Bioinformatics

Techniques

High-Throughput Stool Metaproteomics: Method and Application to Human Specimens – Gonzalez et al. mSystems

Interindividual Variation in Dietary Carbohydrate Metabolism by Gut Bacteria Revealed with Droplet Microfluidic Culture – Villa et al. mSystems

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 30, 2020

Hallo und Guten Morgen from Germany! I hope you are well and have the time and energy to enjoy some microbiome related reading hours. I included a number of interesting reviews, related to mental and general health, soil microbiome and amphibian skin microbiome.
There is also a nice variety of new microbe research, including the influence of temperature changes on the microbiome of lizards and the microbiome’s association with heat tolerance, seasonal cycles of microbial communities in the Baltic Sea and the influence of hydrocarbons pollutants on the human skin microbiome.
Enjoy the reading!

SARS-CoV-2/COVID-19

Preprint: Role of Anti-SARS-CoV-2 antibodies in different cohorts: Can they provide clues for appropriate patient triaging? – Manohar B Mutnal – bioRxiv


General microbiome

Review: Impact of Human Microbiome on Health – Sujata Das – Microbial Diversity, Interventions and Scope

Review: Inflammation in Mental Disorders: Is the Microbiota the Missing Link? – Sophie Ouabbou – Neuroscience Bulletin

Human skin microbiome

Changes of the human skin microbiota upon chronic exposure to polycyclic aromatic hydrocarbon pollutants – Marcus H. Y. Leung – Microbiome

Human gut microbiome

Review: Current Limitations for the Assessment of the Role of the Gut Microbiome for Attention Deficit Hyperactivity Disorder (ADHD) – Andreas Hiergeist – Frontiers in Psychiatry


Animal microbiome

*Lizard gut microbiome changes with temperature and is associated with heat tolerance – Andrew H. Moeller – Applied and Environmental Microbiology

Review: The Amphibian Skin Microbiome and Its Protective Role Against Chytridiomycosis – Eria A. Rebollar – Herpetologica

Bacterial diversity associated with the abdomens of naturally Plasmodium-infected and non-infected Nyssorhynchus darlingi – Tatiane Marques Porangaba Oliveira – BMC Microbiology

Plant, root, and soil microbiome

Review: Deliberate introduction of invisible invaders: A critical appraisal of the impact of microbial inoculants on soil microbial communities – Panji Cahya Mawarda – Soil Biology and Biochemistry

Plant microbiota modified by plant domestication – Esperanza Martínez-Romero – Systematic and Applied Microbiology

Water and extremophile microbiome

A genomic view of trophic and metabolic diversity in clade-specific Lamellodysidea sponge microbiomes – Sheila Podell – Microbiome

Functional Associations and Resilience in Microbial Communities – Maria-Luisa Avila-Jimenez – Microorganisms

*Autumn to spring microbial community in the northern Baltic Sea: temporal variability in bacterial, viral and nanoflagellate abundance during the cold-water season – Laura Kaikkonen – Polar Biology

Food microbiology

Reservoirs of antimicrobial resistance genes in retail raw milk – Jinxin Liu – Microbiome


Bioinformatics

Correlation-Centric Network (CCN) representation for microbial co-occurrence patterns: new insights for microbial ecology – Pengshuo Yang – NAR Genomics and Bioinformatics

Review: From bag-of-genes to bag-of-genomes: metabolic modelling of communities in the era of metagenome-assembled genomes – Clémence Frioux – Computational and Structural Biotechnology Journal

June 29, 2020

Human microbiome

Analysis of the diversity of intestinal microbiome and its potential value as a biomarker in patients with schizophrenia: A cohort study. – Pan et al. – Psychiatry Research

A longitudinal study of the development of the saliva microbiome in infants 2 days to 5 years compared to the microbiome in adolescents. – Holferson et al. – Scientific Reports

Gut microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome. – Levy et al. – PNAS

Genome-wide associations of human gut microbiome variation and implications for causal inference analyses. – Hughes et al. – Nature Microbiology

Cancer and the microbiome. – Ashray Gunjur. The Lancet

Food microbiology

Influences of Ingredients and Bakers on the Bacteria and Fungi in Sourdough Starters and Bread – Reese et al. – mSphere

Plant, root and soil microbiome

Effects of zinc pollution and compost amendment on the root microbiome of a metal tolerant poplar clone. – Guarino et al. – Frontier in Microbioloy

New insights into the distributions of nitrogen fixation and diazotrophs revealed by high-resolution sensing and sampling methods. – Tang et al. – The ISME Journal

Language of plant-microbe-microbe interactions in rhizospheric ecosystems. – Khare et al. – Molecular Aspects of Plant Benefitial Microbes in Agriculture

Environmental microbiology

Editorial: Microbial Ecology in Reservoirs and Lakes. Zhang et al. – Frontier in Microbiology

Natural Holobiome Engineering by Using Native Extreme Microbiome to Counteract the Climate Change Effects. – Rodriguez and Duran – Frontiers in Bioengineering and Biotechnology.

June 28, 2020

Greetings from Wiltshire, England!

Today’s digest brings a little bit of everything. We’ve been cataloguing the latest COVID-19 publications during this pandemic, and today I’m please to bring you a paper combining both COVID-19 and microbiome research!

Elsewhere, there are plenty of environmental microbiome publications, including a great paper on the challenges of studying microbiology in space, an analysis of how aerosols spread COVID-19 and other infectious agents in dental practices, and plenty of articles on various aspects of soil microbiomes.

I hope everyone’s coping well during these times. On a personal level, I’m delighted to be returning to the lab this week to resume my PhD research into gut microbiomes and cancer. I’m glad to be back, but worried about how my pipetting skills have suffered during my time off!

Stay safe, and happy reading!

COVID-19

Intestinal Flora as a Potential Strategy to Fight SARS-CoV-2 Infection – He et al.Frontiers in Microbiology

Preprint: Naturally mutated spike proteins of SARS-CoV-2 variants show differential levels of cell entry – Ozono et al.

Human vaginal microbiome

Novel Potential Probiotic Lactobacilli for Prevention and Treatment of Vulvovaginal Infections – Kumherová et al. – Probiotics and Antimicrobial Proteins

Preprint: The structure and diversity of strain level variation in vaginal bacteria –Tortelli et al.

Human gut microbiome

Early exposure to food contaminants reshapes maturation of the human brain-gut-microbiota axis – Sarron et al.World Journal of Gastroenterology

Luminal microbiota related to Crohn’s disease recurrence after surgery – Hamilton et al.Gut Microbes

Animal experiments

Preprint: The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet – Mims et al.

Animal microbiome

Germ-free housing conditions do not affect aortic root and aortic arch lesion size of late atherosclerotic low-density lipoprotein receptor-deficient mice – Kiouptsi et al.Gut Microbes

The effects of environment and ontogeny on the skin microbiome of two Stegastes damselfishes (Pomacentridae) from the eastern Caribbean Sea – Xavier et al.Marine Biology

Variations and Potential Factors of Gut Prokaryotic Microbiome During Spawning Migration in Coilia nasus – Ying et al.Current Microbiology

Plant, root, and soil microbiome

Genetic diversity of Agrobacterium species isolated from nodules of common bean and soybean in Brazil, Mexico, Ecuador and Mozambique, and description of the new species Agrobacterium fabacearum sp. nov. – Delamuta et al.International Journal of Systematic and Evolutionary Microbiology

Efects of cadmium perturbation on the microbial community structure and heavy metal resistome of a tropical agricultural soil – Salam et al.Bioresources and Bioprocessing

Differences in soil microbial communities and enzyme activity due to the application of bioslurry under cultivation – Mofokeng et al.South African Journal of Plant and Soil

Microbial Communities in the Fynbos Region of South Africa: What Happens during Woody Alien Plant Invasions – Jacobs et al.Diversity

Water and extremophile microbiome

Sierra Nevada mountain lake microbial communities are structured by temperature, resources and geographic location – Schulhof et al.Molecular Ecology

Preprint: Fungal communities in sediments along a depth gradient in the Eastern Tropical Pacific – Rojas-Jimenez et al

Built environment

Preprint: Evaluating aerosol and splatter following dental procedures – Allison et al.

Microbes in space

Current Progression: Application of High-Throughput Sequencing Technique in Space Microbiology – Chen et al.BioMed Research International

Food microbiology

Swine Methicillin-resistant Staphylococcus aureus carrying toxic-shock syndrome toxin gene in Hong Kong, China – Sapugahawatte et al. – Emerging Microbes and Infections

Probiotics / prebiotics

Moving from probiotics to precision probiotics – Veiga, et al. – Nature Microbiology

Phages and viruses

Fetal inheritance of chromosomally integrated human herpesvirus 6 predisposes the mother to pre-eclampsia – Gaccioli et al. – Nature Microbiology

Techniques

Developing standards for the microbiome field – Amos et al.Microbiome

Microbes in the news

Team Examines Microbiome of Marine Invertebrate That Produces Anticancer CompoundTechnology Networks

Bacteria live on our eyeballs — and understanding their role could help treat common eye diseasesYahoo! News

June 27, 2020

Shalom from Israel and a Happy world microbiome day!

Yes, it is a true day! celebrating the huge diversity of microbes around us, above us, below us and inside us. Check the day’s official website for more information, and take the weekend to appreciate this amazing field and your own personal contribution to advancing our knowledge about microbial communities on our planet.

Personally, I did my undergrad in Ecology and Evolution, confidence that I’ll my scientific career will focus on plant ecology and distribution, or at least large animals. Microbiology classes and introduction labs bored me, and I did my best to avoid this topic. But all of a sudden, during my Master’s degree (where I worked on a pathogenicity mechanism of postharvest disease-causing bacteria), I fell in love with microbiology in general, and specific bacterial communities. The huge untapped diversity, the unbelievable functions and the amazing interactions needed to maintain a functional community of these invisible inhabitants just fascinated me. Today, as a Ph.D. student exploring secondary metabolites gene clusters in soil and root microbiome, I’m a super-fan of the bacterial world.

How did you end up being microbiome suckers? Feel free to share your stories here as a comment, on MD FB page, or directly on tweeter.

Today’s digest include several microbimoe papers of animal midels (including ‘dirty mice’), diseased tomatoes taxonomical and functional microbiome profile, AND- a sweet reminder of the pre-COVID-19 world, with an analysis of the dust microbiome of a plane (remember this vehicle?).

Human and Animal Models microbiome

**Microbial transmission in animal social networks and the social microbiome, Amar Sarkar , Nat. Eco. Evo.

Does entry to center-based childcare affect gut microbial colonization in young infants?, Gerben D. A. Hermes, Scientific Reports

Serum metabolites reflecting gut microbiome
alpha diversity predict type 2 diabetes
, Cristina Menni, Gut microbes

**New Insights into the Immune System Using Dirty Mice, Sara E. Hamilton, J. Immunology.

Optimization of cerebrospinal fluid microbial metagenomic sequencing diagnostics,Josefin Olausson , bioRxiv

Sleep fragmentation increases blood pressure and is associated with alterations in the gut microbiome and fecal metabolome in rats, Katherine.Maki, Phys. Geno.

Animal microbiome

Environment Shapes the Microbiome of the Blue Orchard Bee, Osmia lignaria, Hamutahl Cohen, Microbial Ecology

The gut mycobiome of healthy mice is shaped by the environment and shapes metabolic outcomes in response to diet, Tahliyah S. Mims, bioRxiv

Microbial communities network analysis of anaerobic reactors fed with bovine and swine slurry, Eliane Cristina Gruszka Vendruscolo, Sci. Tot. Env.

Metagenomic analysis reveals significant differences in microbiome and metabolic profiles in the rumen of sheep fed low N diet with increased urea supplementation, Zhipeng Li, FEMS Micro. Eco.

Soil and Plant microbiome

Changes in Bacterial and Fungal Microbiomes Associated with Tomatoes of Healthy and Infected by Fusarium oxysporum f. sp. lycopersici, Xin Zhou, Microbial Ecology

Insights into drylands biocrust microbiome: geography, soil depth, and crust type affect biocrust microbial communities and networks in Mojave Desert, USA, Nuttapon Pombubpa, FEMS Micro. Eco.

Exploring the Lignin Catabolism Potential of Soil-Derived Lignocellulolytic Microbial Consortia by a Gene-Centric Metagenomic Approach, Laura Díaz-García, Microbial Ecology

Shotgun Metagenomics Of Dust Microbiome From Flight Deck And Cabin In Civil Aviation Aircraft, Yu Sun, Indoor Air

Bioinformatics

MicroNiche: an R package for assessing microbial niche breadth and overlap from amplicon sequencing data, D.R. Finn , FEMS Micro. Eco.

June 26, 2020

COVID-19

Modelling donor screening strategies to reduce the risk of SARS-CoV-2 via fecal microbiota transplantation – Olesen et al. – bioRxiv

Oral microbiome

Streptococcus mutans adhesion force sensing in multi-species oral biofilms – Wang et al. – npc Biofilms and Microbiomes

Skin microbiome

HGT in the human and skin commensal Malassezia: A bacterially derived flavohemoglobin is required for NO resistance and host interaction – Ianiri et al. – PNAS

Gut-brain axis

The Serotonin Neurotransmitter Modulates Virulence of Enteric Pathogens – Kumar et al. – Cell Host and Microbe

June 25, 2020

COVID19
Structural plasticity of SARS-CoV-2 3CL Mpro active site cavity revealed by room temperature X-ray crystallography – Kneller et al. – Nature Communications

Pregnancy and early life
Review – Maternal and infant factors that shape neonatal gut colonisation by bacteria – O’Neill et al. – Expert Review of Gastroenterology & Hepatology

Perinatal risk factors for fecal antibiotic resistance gene patterns in pregnant women and their infants – Sosa-Moreno et al. – PLOS One

Human gut microbiome
Microbial and metabolomic profiles in correlation with depression and anxiety co-morbidities in diarrhoea-predominant IBS patients – Liu et al. – BMC Microbiology

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

Animal experiments
Effects of Drinking Water Temperature and Flow Rate during Cold Season on Growth Performance, Nutrient Digestibility and Cecum Microflora of Weaned Piglets – Zhang et al. – Animals

Effects of supplementary feeding on the rumen morphology and bacterial diversity in lambs – Lv et al. – PeerJ

Evaluating the association between feed efficiency and the fecal microbiota of early-life Duroc pigs using 16S rRNA sequencing – Si et al. – AMB Express

Establishment and Stability of the Murine Oral Microbiome – Ramos et al. – Journal of Dental Research

Effects of chronic treatment with new strains of Lactobacillus plantarum on cognitive, anxiety- and depressive-like behaviors in male mice – Barros-Santos et al. – PLOS One

Animal microbiome
Reproductive hormones mediate changes in the gut microbiome during pregnancy and lactation in Phayre’s leaf monkeys – Mallott et al. – Scientific Reports

Plant, root, and soil microbiome
Microbial community types and signature-like soil bacterial patterns from fortified prehistoric hills of Thuringia (Germany) – Kohler et al. – Community Ecology

Meta-analysis of the impacts of global change factors on soil microbial diversity and functionality – Zhou et al. – Nature Communications

Prairie plants harbor distinct and beneficial root-endophytic bacterial communities – Adu-Oppong et al. – PLOS One

Water and extremophile microbiome
Surviving marginalized reefs: assessing the implications of the microbiome on coral physiology and survivorship – Roitman et al. – Coral Reefs

Microbial Communities Associated with Farmed Genypterus chilensis: Detection in Water Prior to Bacterial Outbreaks Using Culturing and High-Throughput Sequencing – Levican et al. – Animals

Energy-Efficient Single-Stage Nitrite Shunt Denitrification with Saline Sewage through Concise Dissolved Oxygen (DO) Supply: Process Performance and Microbial Communities – Zhuang et al. – Microorganisms

Food microbiology
Dynamics of Microbial Communities, Texture and Flavor in Suan zuo yu during Fermentation – Wang et al. – Food Chemistry

Probiotics / prebiotics
Bifidobacterium bifidum Suppresses Gut Inflammation Caused by Repeated Antibiotic Disturbance Without Recovering Gut Microbiome Diversity in Mice – Ojima et al. – Frontiers in Microbiology

Bacillus subtilis PB6 based probiotic supplementation plays a role in the recovery after the necrotic enteritis challenge – Aljumaah et al. – PLOS One

Bioinformatics
BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline – Shamsaddini et al. – PLOS One