Category Archives: Animal microbiome

January 14, 2022

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Human and General Microbiome

Intestinal commensal microbiota and cytokines regulate Fut2(+) Paneth cells for gut defense – Mariko Kamioka – PNAS

Gut microbiota promotes cholesterol gallstone formation by modulating bile acid composition and biliary cholesterol secretion – Hai Hu – Nature Communications

Non-typeable Haemophilus influenzae–Moraxella catarrhalis vaccine for the prevention of exacerbations in chronic obstructive pulmonary disease: a multicentre, randomised, placebo-controlled, observer-blinded, proof-of-concept, phase 2b trial – Stefan Andreas – The Lancet. Respiratory Medicine

PET microplastics affect human gut microbiota communities during simulated gastrointestinal digestion, first evidence of plausible polymer biodegradation during human digestion – Alba Tamargo – Scientific Reports

Ear microbiota and middle ear disease: a longitudinal pilot study of Aboriginal children in a remote south Australian setting – Steven L Taylor – BMC Microbiology

Comparative analysis of DNA extraction and PCR product purification methods for cervicovaginal microbiome analysis using cpn60 microbial profiling – Elinor Shvartsman – PloS ONE

Microbial hydrogen economy alleviates colitis by reprogramming colonocyte metabolism and reinforcing intestinal barrier – Li Ge – Gut Microbes

Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome – Dalong Hu – Cell Reports

Draft Genome Sequence of Bifidobacterium adolescentis 4-2, Isolated from Healthy Human Feces – Hend Altaib – Microbiology Resource Announcements

Preview: Diet, microbe, and autism: Cause or consequence? – Guanjian Li – Cell Host & Microbe

Human and General Microbiome – Reviews

Systematic review: Gut microbiota in patients with Alzheimer’s disease spectrum: a systematic review and meta-analysis – Chun-Che Hung – Aging

Systematic review: Characteristics of the gut microbiome in women with gestational diabetes mellitus: A systematic review – Louise Søndergaard Rold – PloS ONE

Systematic review: Respiratory tract infections and gut microbiome modifications: A systematic review – Claire A Woodall – PloS ONE

Systematic review: Repercussions of intermittent fasting on the intestinal microbiota community and body composition: a systematic review – Flaydson C S Pinto – Nutrition Reviews

Review: Skin Deep: The Role of the Microbiota in Cutaneous Autoimmunity – Márcia S Pereira – The Journal of Investigative Dermatology

Review: Current advances in the anti-inflammatory effects and mechanisms of natural polysaccharides – Dan Yuan – Critical Reviews in Food Science and Nutrition

Animal Microbiome

The gut microbiota of environmentally enriched mice regulates visual cortical plasticity – Leonardo Lupori – Cell Reports

Characterization of the juvenile koala gut microbiome across wild populations – Michaela D J Blyton – Environmental Microbiology

Specific gut bacterial responses to natural diets of tropical birds – Kasun H Bodawatta – Scientific Reports

Effect of dietary supplementation of lauric acid on growth performance, antioxidative capacity, intestinal development and gut microbiota on black sea bream (Acanthopagrus schlegelii) – Sami Ullah – PloS ONE

Establishment and resilience of transplanted gut microbiota in aged mice – Ying Wang – iScience

Identification of Gut Bacteria such as Lactobacillus johnsonii that Disseminate to Systemic Tissues of Wild Type and MyD88-/- Mice – Sreeram Udayan – Gut Microbes

Responsive changes of rumen microbiome and metabolome in dairy cows with different susceptibility to subacute ruminal acidosis – Tao Zhang – Animal Nutrition

Torula yeast in the diet of Atlantic salmon Salmo salar and the impact on growth performance and gut microbiome – Alexandra Leeper – Scientific Reports

Distinct gut microbiomes in two polar bear subpopulations inhabiting different sea ice ecoregions – Megan Franz – Scientific Reports

Microbiome Resilience despite a Profound Loss of Minority Microbiota following Clindamycin Challenge in Humanized Gnotobiotic Mice – Lin Liu – Microbiology Spectrum

Review: Bovine respiratory microbiota of feedlot cattle and its association with disease – Jianmin Chai – Veterinary Research

Plant Microbiome

Plant neighborhood shapes diversity and reduces interspecific variation of the phyllosphere microbiome – Kyle M Meyer – The ISME Journal

Environmental Microbiome

Sulfate-dependant microbially induced corrosion of mild steel in the deep sea: a 10-year microbiome study – Pauliina Rajala – Microbiome

Microbial community composition and glyphosate degraders of two soils under the influence of temperature, total organic carbon and pH – Angelica M Muskus – Environmental Pollution

Increased Tea Saponin Content Influences the Diversity and Function of Plantation Soil Microbiomes – Shouke Zhang – Microbiology Spectrum

Bioinformatics

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO – Britta Velten – Nature Methods

Review: Inferring microbiota functions from taxonomic genes: a review – Christophe Djemiel – GigaScience

January 12, 2022

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General microbiome

[PERSPECTIVE]It’s the Economy, Stupid: Applying (Micro)economic Principles to Microbiome Science – Kashtan, Bushong and Leveau – mSystems

[PERSPECTIVE]Conceptual Exchanges for Understanding Free-Living and Host-Associated Microbiomes – Pfister et al. – mSystems

Human endometrial microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Moreno et al. – Microbiome

Human oral microbiome

[REVIEW]Temporal development of the infant oral microbiome – Blum et al. – Critical Reviews in Microbiology

Human gut microbiome

Effect of antibiotic pretreatment on bacterial engraftment after Fecal Microbiota Transplant (FMT) in IBS-D – Singh et al. – Gut Microbes

[REVIEW]The gut microbiota can orchestrate the signaling pathways in colorectal cancer – Bennedsen et al. – Journal of Pathology, Microbiology and Immunology

Age-Associated Gut Dysbiosis, Marked by Loss of Butyrogenic Potential, Correlates With Altered Plasma Tryptophan Metabolites in Older People Living With HIV – Ghare et al. – Journal of Acquired Immune Deficiency Syndrome

Intestinal Microbiota and Host Cooperate for Adaptation as a Hologenome – Zhou et al. – mSystems

The bacterial density of clinical rectal swabs is highly variable, correlates with sequencing contamination, and predicts patient risk of extraintestinal infection – Chanderraj et al. – Microbiome

Animal microbiome

Consistent changes in the intestinal microbiota of Atlantic salmon fed insect meal diets – Li et al. – Animal Microbiome

Maternal regulation of biliary disease in neonates via gut microbial metabolites – Jee et al. – Nature Communications

Reduced calorie diet combined with NNMT inhibition establishes a distinct microbiome in DIO mice – Dimet-Wiley et al. – Scientific Reports

Comparison of Gut Microbiota and Metabolic Status of Sows With Different Litter Sizes During Pregnancy – Chen et al. – Front. Vet. Sci.

Modulation of gut microbiota impacts diet-induced and drug-induced alopecia in mice – Lam et al. – Gut

Sex-specific differences in the gut microbiota and fecal metabolites in an adolescent valproic acid-induced rat autism model – Gu et al. – Frontiers in Bioscience Landmark

Host tp53 mutation induces gut dysbiosis eliciting inflammation through disturbed sialic acid metabolism – Lee et al. – Microbiome

Plant, root, and soil microbiome

Whole-Genome Duplication and Host Genotype Affect Rhizosphere Microbial Communities – Ponsford et al. – mSystems

Bioinformatics

A Goldilocks Principle for the Gut Microbiome: Taxonomic Resolution Matters for Microbiome-Based Classification of Colorectal Cancer – Armour et al. – mBio

Towards a metagenomics machine learning interpretable model for understanding the transition from adenoma to colorectal cancer – Casimiro-Soriguer et al. – Scientifi Reports

Techniques

[PREPRINT]Library Preparation and Sequencing Platform Introduce Bias in Metagenomic-Based Characterizations of Microbiomes – Poulsen et al. – bioRxiv

January 10, 2022

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Today’s digest features studies on glycosaminoglycans degradation by urinary microbiome, social network of honeybees, improved DNA extraction for low biomass samples, the LotuS2 tool for amplicon sequencing analysis, and more. Happy Monday!

Gut microbiome

Review: The role of the microbiota in the management of intensive care patients – Piotr Szychowiak – Annals of Intensive Care

Review: The Gut Microbiome in Myalgic Encephalomyelitis (ME)/Chronic Fatigue Syndrome (CFS) – Rahel S. König – Frontiers in Immunology

Review: Opioid Use, Gut Dysbiosis, Inflammation, and the Nervous System – Richa Jalodia – Journal of Neuroimmune Pharmacology

Urinary microbiome

*A Semi-Quantitative Assay to Measure Glycosaminoglycan Degradation by the Urinary Microbiota – Vivian H. Nguyen – Frontiers in Cellular and Infection Microbiology

Vaginal microbiome

Composition and Stability of the Vaginal Microbiota of Pregnant Women With Inflammatory Bowel Disease – Janet E Hill – Inflammatory Bowel Diseases

Skin microbiome

*Anatomy promotes neutral coexistence of strains in the human skin microbiome – Arolyn Conwill – Cell Host & Microbe

Water microbiome

Tenets of a Holistic Approach to Drinking Water-Associated Pathogen Research, Management, and Communication – Caitlin Proctor – Water Research

Animal microbiome

Review: Possibilities and limits for using the gut microbiome to improve captive animal health – Jessica Diaz & Aspen T. Reese – Animal Microbiome

The mosquito microbiome includes habitat-specific but rare symbionts – Hans Schrieke – Computational and Structural Biotechnology Journal

*The gut microbiota affects the social network of honeybees – Joanito Liberti – bioRxiv

Techniques and methods

Combined assembly of long and short sequencing reads improve the efficiency of exploring the soil metagenome – Guoshun Xu – BMC Genomics

Enrichment of gut microbiome strains for cultivation-free genome sequencing using droplet microfluidics – Anna Pryszlak – Cell Report Methods

When to suspect contamination rather than colonization – lessons from a putative fetal sheep microbiome – Simone Bihl – Gut Microbes

*Microvolume DNA extraction methods for microscale amplicon and metagenomic studies – Anna R. Bramucci – ISME Communications

Bioinformatics

*LotuS2: An ultrafast and highly accurate tool for amplicon sequencing analysis – Ezgi Özkurt – bioRxiv

Generating lineage-resolved, complete metagenome-assembled genomes from complex microbial communities – Derek M. Bickhart – Nature Biotechnology

January 7, 2022

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Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

January 6, 2022

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Human and General Microbiome

Mendelian randomization analyses support causal relationships between blood metabolites and the gut microbiome – Xiaomin Liu – Nature Genetics

Determine independent gut microbiota-diseases association by eliminating the effects of human lifestyle factors – Congmin Zhu – BMC Microbiology

Comparing Published Gut Microbiome Taxonomic Data Across Multinational Studies – Brianna K Meeks – Nursing Research

A Comprehensive Review on the Role of the Gut Microbiome in Human Neurological Disorders – Shokufeh Ghasemian Sorboni – Clinical Microbiology Reviews

Beneficial Microbes and Compounds

Lactobacillus casei Zhang exerts anti-obesity effect to obese glut1 and gut-specific-glut1 knockout mice via gut microbiota modulation mediated different metagenomic pathways – Qiuwen He – European Journal of Nutrition

Administration of Human Derived Upper gut Commensal Prevotella histicola delays the onset of type 1 diabetes in NOD mice – Eric Marietta – BMC Microbiology

Probiotic supplementation in neonates with congenital gastrointestinal surgical conditions: a pilot randomised controlled trial – Shripada Rao – Pediatric Research

Dietary supplementation with low-dose xylooligosaccharide promotes the anti-Salmonella activity of probiotic Lactiplantibacillus plantarum ZS2058 in a murine model – Junsheng Liu – Food Research International 

Review: Recent understanding of human milk oligosaccharides in establishing infant gut microbiome and roles in immune system – Ravindra Pal Singh – Food Research International

Microbiome and Metabolism

Gut Microbiota Diversity and Overweight/Obesity in Infancy: Results from a Nested Case-control Study – Hong Mei – Current Medical Science

Microbiome and Cancer

Microbiome composition indicate dysbiosis and lower richness in tumor breast tissues compared to healthy adjacent paired tissue, within the same women – Maria Valeria Esposito – BMC Cancer

Changes in the gut bacterial communities in colon cancer surgery patients: an observational study – Mohamed Abbas – Gut Pathogens

Urinary and Reproductive Tract Microbiome

Endometrial microbiota composition is associated with reproductive outcome in infertile patients – Inmaculada Moreno – Microbiome

Dysbiosis of vaginal microbiota associated with persistent high-risk human papilloma virus infection – Ling Mei – Journal of Translational Medicine

Urogenital Microbiota:Potentially Important Determinant of PD-L1 Expression in Male Patients with Non-muscle Invasive Bladder Cancer – Chunxiao Chen – BMC Microbiology

Animal Microbiome

Destabilization of the Bacterial Interactome Identifies Nutrient Restriction-Induced Dysbiosis in Insect Guts – Ramona Marasco – Microbiology Spectrum

Specific Strains of Honeybee Gut Lactobacillus Stimulate Host Immune System to Protect against Pathogenic Hafnia alvei – Haoyu Lang – Microbiology Spectrum

Characterization of captive and wild 13-lined ground squirrel cecal microbiotas using Illumina-based sequencing – Edna Chiang – Animal Microbiome

Metagenomic and metatranscriptomic analyses reveal minor-yet-crucial roles of gut microbiome in deep-sea hydrothermal vent snail – Yi Yang – Animal Microbiome

Host, microbiome, and complex space: applying population and landscape genetic approaches to gut microbiome research in wild populations – Claire E Couch – The Journal of Heredity

Antibiotic resistance and potential bacterial pathogens identified in red deer’s faecal DNA – Diana Dias – Transboundary and Emerging Diseases

Review: Gut microbiome-immune system interaction in reptiles – Ruqaiyyah Siddiqui – Journal of Applied Microbiology

Plant and Soil Microbiome

Contrasting Effects of Local Environmental and Biogeographic Factors on the Composition and Structure of Bacterial Communities in Arid Monospecific Mangrove Soils – T Thomson – Microbiology Spectrum

Review: Endophytic Microbiota of Rice and Their Collective Impact on Host Fitness – Santosh Kumar Jana – Current Microbiology

Other Microbes

Spaceflight Virology: What Do We Know about Viral Threats in the Spaceflight Environment? – Bruno Pavletić – Astrobiology

Microbiome Analysis Methods

Cell-Free Paper-Based Analysis of Gut Microbiota and Host Biomarkers – Melissa K Takahashi – Methods in Molecular Biology 

Bioinformatics

CACONET: a novel classification framework for microbial correlation networks – Yuanwei Xu – Bioinformatics

January 4, 2022

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Happy new year! Today’s digest is jam packed with articles published over the Christmas period. This includes the Skin Microbial Genome Collection (SMGC), a fascinating study linking the gut virome to rotavirus vaccine response, multiple cancer-microbiome papers and a catalogue of the human gut archaeome

General microbiome

The Metaproteomics Initiative: a coordinated approach for propelling the functional characterization of microbiomes – Bossche et al. Microbiome

Directional Gaussian Mixture Models of the Gut Microbiome Elucidate Microbial Spatial Structure – Pasarkar et al. mSystems

Human gut microbiome

Human gut-microbiome-derived propionate coordinates proteasomal degradation via HECTD2 upregulation to target EHMT2 in colorectal cancer – Ryu et al. ISME

Gut microbiomes from Gambian infants reveal the development of a non-industrialized Prevotella-based trophic network – Goffau et al. Nature Microbiology.

Reuterin in the healthy gut microbiome suppresses colorectal cancer growth through altering redox balance – Bell et al. Cancer Cell. 

Population study of the gut microbiome: associations with diet, lifestyle, and cardiometabolic disease – Walker et al. Genome Medicine

Enteric virome negatively affects seroconversion following oral rotavirus vaccination in a longitudinally sampled cohort of Ghanaian infants – Kim et al. Cell Host & Microbe

Maternal gut bacteria drive intestinal inflammation in offspring with neurodevelopmental disorders by altering the chromatin landscape of CD4+ T cells – Kim et al. Immunity

Lactobacillus gallinarum modulates the gut microbiota and produces anti-cancer metabolites to protect against colorectal tumourigenesis – Sugimura et al. Gut

A catalogue of 1,167 genomes from the human gut archaeome – Chibani et al. Nature Microbiology

Variation and transmission of the human gut microbiota across multiple familial generations – Valles-Colomer et al. Nature Microbiology. 

The Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping – Beresford-Jones et al. Cell Host & Microbe

Human skin & oral microbiome

Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions – Kashaf et al. Nature Microbiology.

Alterations of human skin microbiome and expansion of antimicrobial resistance after systemic antibiotics – Jo et al. Science Translational Medicine

Microbiome-mediated incapacitation of interferon lambda production in the oral mucosa – Rodriguez-Hernandez et al. PNAS

Plant microbiome

Glutamic acid reshapes the plant microbiota to protect plants against pathogens – Kim et al. Microbiome. 

Water microbiome

Metagenomics of Antarctic Marine Sediment Reveals Potential for Diverse Chemolithoautotrophy – Garber et al. mSphere

Dissecting the dominant hot spring microbial populations based on community-wide sampling at single-cell genomic resolution – Bowers et all. ISME

Bioinformatics

Fast and accurate metagenotyping of the human gut microbiome with GT-Pro – Shi et al. Nature Biotechnology

Rapid screening and identification of viral pathogens in metagenomic data – Song et al. BMC Medical Genomics. 

December 22, 2021

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General microbiome

[PREPRINT]Unconstrained coevolution of bacterial size and the latent period of plastic phage – Bonachela, Choua & Heath – bioRxiv

Not a ‘they’ but a ‘we’: the microbiome helps promote our well-being – Ragsdale – Journal of Biological Chemistry

Microbial metabolite delta-valerobetaine is a diet-dependent obesogen – Liu et al. – Nature Metabolism

[EDITORIAL]15 years of microbial biotechnology: the time has come to think big—and act soon – de Lorenzo – Microbial Biotechnology

Pregnancy and early life

Microbial community networks across body sites are associated with susceptibility to respiratory infections in infants – Reyman et al. – Communications Biology

Human oral microbiome

Profiling the oral microbiomes in patients with Alzheimer’s disease – Guo et al. – Oral Diseases

Human skin microbiome

[REVIEW]Human Skin Microbiota in Health and Disease – Bay & Ring – Journal of Pathology, Microbiology and Immunology

Human vaginal microbiome

Human implantation: The complex interplay between endometrial receptivity, inflammation, and the microbiome – Sehring & Jeelani – Placenta

Large-scale characterisation of the pregnancy vaginal microbiome and sialidase activity in a low-risk Chinese population – Ng et al. – NPJ Biofilms and Microbiomes

Human gut microbiome

The potential of gut microbiome as a non-invasive predictive biomarker for early detection of pancreatic cancer and hepatocellular carcinoma – Kaźmierczak-Siedlecka – European Review for Medical and Pharmacological Sciences

The effect of antibiotics on the human microbiome: a systematic review – van Zyl et al. – International Journal of Antimicrobial Agents

[REVIEW]Non-alcoholic fatty liver disease: the interplay between metabolism, microbes and immunity – Tilg et al. – Nature Metabolism

Clinical efficacy of fecal microbial transplantation treatment in adults with moderate-to-severe atopic dermatitis – Mashiah et al. – Immunity, Inflammation and Disease

Deviated and early unsustainable stunted development of gut microbiota in children with autism spectrum disorder – Lou et al. – Gut

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Oat Fiber Modulates Hepatic Circadian Clock via Promoting Gut Microbiota-Derived Short Chain Fatty Acids – Han et al. – J. Agric. Food Chem.

Animal microbiome (for animals in the wild)

Effects of sublethal azadirachtin on the immune response and midgut microbiome of Apis cerana cerana (Hymenoptera: Apidae) – Zhao et al. – Ecotoxicology and Environmental Safety

Analysis of the microbial diversity in the fecal material of the critically endangered African wild dog, Lycaon pictus – Sanches et al. – Archives of Microbiology

Divergence together with microbes: A comparative study of the associated microbiomes in the closely related Littorina species – Maltseva et al. – PLOS One

Gut microbiome composition, not alpha diversity, is associated with survival in a natural vertebrate population – Worsley et al. – Animal Microbiome

Clinical health issues, reproductive hormones, and metabolic hormones associated with gut microbiome structure in African and Asian elephants – Keady et al. – Animal Microbiome

Early life skin microbial trajectory as a function of vertical and environmental transmission in Bornean foam-nesting frogs – McGrath-Blaser et al. – Animal Microbiome

Plant, root, and soil microbiome

[PRERPINT]Disentangling the genetic basis of rhizosphere microbiome assembly in tomato – Oyserman et al. – bioRxiv

[PREPRINT]Amino acid availability determines plant immune homeostasis in the rhizosphere microbiome – Liu et al. – bioRxiv

Techniques

Ancient Metagenomic Studies: Considerations for the Wider Scientific Community – der Sarkissian et al. – mSystems

Assessing the impact of storage time on the stability of stool microbiota richness, diversity, and composition – Holzhausen et al. – Gut Pathogens

December 20, 2021

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Today’s digest is a grab bag that includes research articles on the vaginal microbiota, the gut microbiota of dairy calves, microbial loads in medical waste, and more! I’ve also highlighted a non-microbiology article that found that pet dog owners were significantly less depressed than non-pet owners during the pandemic. So if you’re looking for more reasons to adopt a new furry friend, you can add this one to the list!

General microbiome

Genomic comparison and phenotypic profiling of small colony variants of Burkholderia pseudomallei – Zulkefli et al. – PLOS One

Human vaginal microbiome

Vaginal microbiota of American Indian women and associations with measures of psychosocial stress – Borgogna et al. – PLOS One

Human gut microbiome

Gut microbiota features associated with Clostridioides difficile colonization in dairy calves – Redding et al. – PLOS One

Animal microbiome

Culicoides Latreille (Diptera: Ceratopogonidae) as potential vectors for Leishmania martiniquensis and Trypanosoma sp. in northern Thailand – Sunantaraporn et al. – PLOS Neglected Tropical Diseases

Migratory wild birds carrying multidrug-resistant Escherichia coli as potential transmitters of antimicrobial resistance in China – Yuan et al. – PLOS One

Plant, root, and soil microbiome

Characterization of soils conducive and non-conducive to Prunus replant disease – Khan et al. – Plos One

Built environment

Disposal habits and microbial load of solid medical waste in sub-district healthcare facilities and households in Yilo-Krobo municipality, Ghana – Egbenyah et al. – PLOS One

Phages and viruses

A systematic review and meta-analysis of the potential non-human animal reservoirs and arthropod vectors of the Mayaro virus – Celone et al. – PLOS Neglected Tropical Diseases

Bioinformatics

Genomic prediction using low-coverage portable Nanopore sequencing – Lamb et al. – PLOS One

Development of an efficient Sanger sequencing-based assay for detecting SARS-CoV-2 spike mutations – Lim et al. – PLOS One

Kara’s non-microbiology pick

***Depression, anxiety, and happiness in dog owners and potential dog owners during the COVID-19 pandemic in the United States – Martin et al. – PLOS One

December 15, 2021

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Nasal microbiome

Deep nasal sinus cavity microbiota dysbiosis in Parkinson’s disease – Pal et al – NPJ Parkinson’s disease

Pregnancy and early life

Influence of Family Integrated Care on the Intestinal Microbiome of Preterm Infants With Necrotizing Enterocolitis and Enterostomy: A Preliminary Study – Yang et al. – Front. Pediatr.

Multi-site human microbiome

[PREPRINT]Alternations of fecal microbes and lung tissue microbes in Lung Cancer patients is more consistent than that of sputum – Yanze et al. – bioRxiv

Human oral microbiome

[PREPRINT]A core salivary microbiome shows the high prevalence of bacterial members yet variability across human populations – Ruan et al. – bioRxiv

Human eye microbiome

Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease – Liang et al. – Front. Cell Dev. Biol.

Human vaginal microbiome

[REVIEW]Beyond bacterial vaginosis: vaginal lactobacilli and HIV risk – Armstrong & Kaul – Microbiome

Human gut mycobiome/microbiome

The fecal mycobiome in non-alcoholic fatty liver disease – Demir et al. – Journal of Hepatology

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Intermittent Fasting Reshapes the Gut Microbiota and Metabolome and Reduces Weight Gain More Effectively Than Melatonin in Mice – Liu et al. – Front. Nutr.

Analyzing gut microbiota composition in individual Anopheles mosquitoes after experimental treatment – Fofana et al. – iScience

Microbial interaction-driven community differences as revealed by network analysis – Pan et al. – Computational and Structural Biotechnology Journal

[PREPRINT]Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle – Hoces et al. – bioRxiv

[PREPRINT]Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina et al – bioRxiv

Gut microbiota modulates weight gain in mice after discontinued smoke exposure – Fluhr et al. – Nature

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

[PREPRINT]Stratified microbial communities are highly sensitive towards multiple combined global change factors, revealing antagonistic and synergistic effects – Suleiman et al. – bioRxiv

Bioinformatics / Databases

Cow Rumen v1.0 – Database

[REVIEW]A review of computational tools for generating metagenome-assembled genomes from metagenomic sequencing data – Yang et al. – Computational and Structural Biotechnology Journal

Microbiome podcast

The Microbiome Facts, Not the Hype – Kristina Campbell

December 08, 2021

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General microbiome

Clinical medicine journals lag behind science journals with regards to “microbiota sequence” data availability – Pryor et al. – Clinical and Translational Medicine

Role of the Microbiome in Regulating Bone Metabolism and Susceptibility to Osteoporosis – Cronin et al. – Calcified Tissue International

Defining and quantifying the core microbiome: Challenges and prospects – Neu, Allen & Roy – PNAS

Clean room microbiome complexity impacts planetary protection bioburden – Hendrickson et al. – Microbiome

[PREPRINT]Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment – Bischofberger & Hall – bioRxiv

Microbiota and stress: a loop that impacts memory – Kraimi et al. – Psychoneuroendocrinology

Species- and site-specific genome editing in complex bacterial communities – Rubin et al. – Nature Microbiology

Human respiratory microbiome

Integrated metabolic and microbial analysis reveals host–microbial interactions in IgE-mediated childhood asthma – Chiu et al. – Scientific Reports

Human oral microbiome

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome – Liu et al. – Cell Discovery

Human gut microbiome

Interaction Between Intestinal Microbiota, Immunology Molecular Mimicry, and AID – Pan et al. – Journal of Immunology Research

[REVIEW]The Gut Microbiome and Hepatocellular Carcinoma – Akkiz – Journal of Gastrointestinal Cancel

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn’s disease – Lee et al. – International Journal of Systematic and Evolutionary Microbiology

Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers – Mao et al. – Journal for ImmunoTherapy of Cancer

Animal experiments (mouse/rat experiments, chickens/pigs on different diets)

Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota – Palomba et al. – NPJ Biofilms and Microbiomes

Animal microbiome (for animals in the wild)

Diet-driven mercury contamination is associated with polar bear gut microbiota – Watson et al. – Scientific Reports

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development – Blyton et al. – Environmental Microbiology

[PREPRINT]Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi – McMurtie et al. – bioRxiv

Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis) – Yao et al. – BioMed Research International

Water and extremophile microbiome (sea, rivers, lakes, glaciers, permafrost, high-salt)

Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site – Court et al. – Microbiology

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation – Iasakov et al. – Marine Environmental Research

Bioinformatics

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis – Sun et al. – Bioinformatics

Techniques

Microbiome Methods in Experimental Autoimmune Encephalomyelitis – Daberkow et al. – Current Protocols

[PREPRINT]A wipe-based stool collection and preservation kit for microbiome community profiling – Hua et al. – bioRxiv