January 17, 2022

Human and General Microbiome

Exploring the universal healthy human gut microbiota around the World – Samuel Piquer-Esteban – Computational and Structural Biotechnology Journal

An Investigation into the Effects of Outer Membrane Vesicles and Lipopolysaccharide of Porphyromonas gingivalis on Blood-Brain Barrier Integrity, Permeability, and Disruption of Scaffolding Proteins in a Human in vitro Model – Anna Barlach Pritchard – Journal of Alzheimer’s Disease

Evolution of fluoroquinolone-resistant Escherichia coli in the gut after ciprofloxacin treatment – V de Lastours – International Journal of Medical Microbiology

Impact of Helicobacter pylori infection on fluid duodenal microbial community structure and microbial metabolic pathways – Tadashi Maeda – BMC Microbiology

Human and General Microbiome – Reviews

Review: Implications of the Gut Microbiome in Sports – Gerardo Miranda-Comas – Sports Health

Review: Gut microbiome effects on neuronal excitability & activity: Implications for epilepsy – Henry Darch – Neurobiology of Disease

Review: The interplay between Sleep and Gut Microbiota – Mengqi Han – Brain Research Bulletin

Animal Microbiome

High-sugar, high-fat, and high-protein diets promote antibiotic resistance gene spreading in the mouse intestinal microbiota – Rong Tan – Gut Microbes

Determinants for antimicrobial resistance genes in farm dust on 333 poultry and pig farms in nine European countries – Roosmarijn Ec Luiken – Environmental Research

In vitro models of the canine digestive tract as an alternative to in vivo assays: Advances and current challenges – Charlotte Deschamps – ALTEX

Review: Do gastrointestinal microbiomes play a role in bats’ unique viral hosting capacity? – Devin N Jones – Trends in Microbiology

Beneficial Microbes and Compounds

A natural polyphenol exerts antitumor activity and circumvents anti-PD-1 resistance through effects on the gut microbiota – Meriem Messaoudene – Cancer Discovery

Amino acid intake and plasma concentrations and their interplay with gut microbiota in vegans and omnivores in Germany – Stefan Dietrich – European Journal of Nutrition

Plant Microbiome

Cytokinin-microbiome interactions regulate developmental functions – Rupali Gupta – Environmental Microbiome

Bioinformatics / Techniques

Quantitative metaproteomics and activity-based protein profiling of patient fecal microbiome identifies host and microbial serine-type endopeptidase activity associated with ulcerative colitis – Peter S Thuy-Boun – Molecular & Cellular Proteomics

Preprint: ProtFinder: finding subcellular locations of proteins using protein interaction networks – Aayush Grover – BioRxiv

January 14, 2022

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 influenzaeMoraxella 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 6, 2022

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

December 24, 2021

Happy Holidays from the MicrobiomeDigest Team!

Human and General Microbiome

Dietary fiber and probiotics influence the gut microbiome and melanoma immunotherapy response – Christine N Spencer – Science 

Association of the gut microbiota and fecal short-chain fatty acids with skeletal muscle mass and strength in children – Fengyan Chen – FASEB Journal

Characteristics of Fecal Microbiota and Machine Learning Strategy for Fecal Invasive Biomarkers in Pediatric Inflammatory Bowel Disease – Xinqiong Wang – Frontiers in Cellular and Infection Microbiology

The microbial gbu gene cluster links cardiovascular disease risk associated with red meat consumption to microbiota L-carnitine catabolism – Jennifer A Buffa – Nature Microbiology

Gut Microbiota Exceeds Cervical Microbiota for Early Diagnosis of Endometriosis – Liujing Huang – Frontiers in Cellular and Infection Microbiology

Natural selection for imprecise vertical transmission in host-microbiota systems – Marjolein Bruijning – Nature Ecology & Evolution

Comparison of the airway microbiota in children with chronic suppurative lung disease – Bushra Ahmed – BMJ Open Respiratory Research

VicRK and CovR polymorphisms in Streptococcus mutans strains associated with cardiovascular infections – Letícia T Oliveira – Journal of Medical Microbiology

Oral Colonization by Entamoeba gingivalis and Trichomonas tenax: A PCR-Based Study in Health, Gingivitis, and Periodontitis – Alaa Yaseen – Frontiers in Cellular and Infection Microbiology

Human and General Microbiome – Reviews

Systematic Review: Probiotics Evaluation in Oncological Surgery: A Systematic Review of 36 Randomized Controlled Trials Assessing 21 Diverse Formulations – Elise Cogo – Current Oncology

Review: Untangling human milk oligosaccharides and infant gut microbiome – Andrea C Masi – iScience

Review: Periodontal Disease: The Good, The Bad, and The Unknown – Lea M Sedghi – Frontiers in Cellular and Infection Microbiology

Review: Clinical implications of preterm infant gut microbiome development – David B Healy – Nature Microbiology

COVID19 and Microbiome

Genomic characterization of the dominating Beta variant carrying vaccinated (Oxford-AstraZeneca) and non-vaccinated COVID-19 patient samples in Bangladesh: A metagenomics and whole genome approach – Md Mizanur Rahaman – Journal of Medical Virology

Animal Microbiome

Concepts and Consequences of a Core Gut Microbiota for Animal Growth and Development – Daphne Perlman – Annual Review of Animal Biosciences

Playing by their own rules: the vertebrate archaeome – Sarah M Hird – Trends in Microbiology

Integration of whole genome sequencing and transcriptomics reveals a complex picture of the reestablishment of insecticide resistance in the major malaria vector Anopheles coluzzii – Victoria A Ingham – PLoS Genetics

Comparative Study of Intestinal Microbiota Composition of Six Edible Fish Species – Tamir Ofek – Frontiers in Microbiology

Captivity Influences the Gut Microbiome of Rhinopithecus roxellana – Xiaochen Wang – Frontiers in Microbiology

Assessment of Changes in the Oral Microbiome That Occur in Dogs with Periodontal Disease – Rodrigo Santibáñez – Veterinary Sciences

Beneficial Microbes and Compounds

Evaluation of Microbiome Alterations Following Consumption of BIOHM, a Novel Probiotic – Mahmoud A Ghannoum – Current Issues in Molecular Biology

Lactobacillus rhamnosus attenuates Thai chili extracts induced gut inflammation and dysbiosis despite capsaicin bactericidal effect against the probiotics, a possible toxicity of high dose capsaicin – Wimonrat Panpetch – PloS ONE

Plant and Soil Microbiome

May the dark be with roots: A perspective on how root illumination may bias in vitro research on plant-environment interactions – Javier Cabrera – The New Phytologist

Site and land-use associations of soil bacteria and fungi define core and indicative taxa – Gschwend Florian – FEMS Microbiology Ecology

Bioinformatics

tascCODA: Bayesian Tree-Aggregated Analysis of Compositional Amplicon and Single-Cell Data – Johannes Ostner – Frontiers in Genetics

December 17, 2021

Human and General Microbiome

Association of microbial dynamics with urinary estrogens and estrogen metabolites in patients with endometriosis – Nhung Le – PloS ONE

Gut Microbiome in Probable Intestinal Tuberculosis and Changes following Anti-Tuberculosis Treatment – Hyuk Yoon – Yonsei Medical Journal

Uncovering the Role of Gut Microbiota in Amino Acid Metabolic Disturbances in Heart Failure Through Metagenomic Analysis – Tomohiro Hayashi – Frontiers in Cardiovascular Medicine

Cerebrospinal Fluid from Healthy Pregnant Women Does Not Harbor a Detectable Microbial Community – Yongyong Kang – Microbiology Spectrum

Stability of healthy subgingival microbiome across space and time – Ryan Tamashiro – Scientific Reports

Successional Stages in Infant Gut Microbiota Maturation – Leen Beller – mBio

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Peng Zhang – The ISME Journal

Bacterial vaginosis and health-associated bacteria modulate the immunometabolic landscape in 3D model of human cervix – Paweł Łaniewski – NPJ Biofilms and Microbiomes

Acute malnutrition and its determinants of preschool children in Bangladesh: gender differentiation – Md Reazul Karim – BMC Pediatrics

SARS-CoV-2 infection reduces human nasopharyngeal commensal microbiome with inclusion of pathobionts – M Nazmul Hoque – Scientific Reports

Gut Mycobiota Dysbiosis in Pulmonary Tuberculosis Patients Undergoing Anti-Tuberculosis Treatment – Demin Cao – Microbiology Spectrum

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid – Michael E J Buhl – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Review: The Role of Gut Microbiota and Genetic Susceptibility in the Pathogenesis of Pancreatitis – Fumin Xu – Gut and Liver

Review: Transcript host-RNA signatures to discriminate bacterial and viral infections in febrile children – Danilo Buonsenso – Pediatric Research

Review: The role of anaerobic bacteria in the development and prevention of colorectal cancer: A review study – Mehrdad Mohammadi – Anaerobe

Review: Lung microbiome, gut-lung axis and chronic obstructive pulmonary disease – Kuppan Gokulan – Current Opinion in Pulmonary Medicine

Systematic review: Gut microbiota modulation as a possible mediating mechanism for fasting-induced alleviation of metabolic complications: a systematic review – Pooneh Angoorani – Nutrition & Metabolism

Systematic review: The relation between the gut microbiome and osteoarthritis: A systematic review of literature – Emanuele Chisari – PloS ONE

Outlook: Ovarian cancer and the microbiome: a complex relationship – Julianna Photopoulos – Nature

Beneficial Microbes and Compounds

Oligofructose-enriched inulin intake, gut microbiome characteristics and the V̇O2peak response to high-intensity interval training in healthy inactive adults – Camilla J Williams – The Journal of Nutrition

Lactiplantibacillus plantarum DMDL 9010 alleviates dextran sodium sulfate (DSS)-induced colitis and behavioral disorders by facilitating microbiota-gut-brain axis balance – Yan-Yan Huang – Food & Function

Long-Term Effects of a Web-Based Low-FODMAP Diet Versus Probiotic Treatment for Irritable Bowel Syndrome, Including Shotgun Analyses of Microbiota: Randomized, Double-Crossover Clinical Trial – Dorit Vedel Ankersen – Journal of Medical Internet Research

Effect of dietary selenium intake on gut microbiota in older population in Enshi region – Zi-Xiong Zhang – Genes and Environment

Animal Microbiome

The bacterial biome of ticks and their wildlife hosts at the urban-wildland interface – Siobhon L Egan – Microbial Genomics

The gut microbiota of wild wintering great bustard (Otis tarda dybowskii): survey data from two consecutive years – Zhiyuan Lu – PeerJ

You are more than what you eat: potentially adaptive enrichment of microbiome functions across bat dietary niches – Melissa R Ingala – Animal Microbiome

Long-term gut microbiome dynamics in Drosophila melanogaster reveal environment-specific associations between bacterial taxa at the family level – Rupert Mazzucco – Proceedings of the Royal Society B. Biological Sciences

Plant and Fungi Microbiome

The Edible Plant Microbiome represents a diverse genetic reservoir with functional potential in the human host – Maria J Soto-Giron – Scientific Reports

Autotoxin Rg(1) Induces Degradation of Root Cell Walls and Aggravates Root Rot by Modifying the Rhizospheric Microbiome – Yanguo Xu – Microbiology Spectrum

Multitrophic Interactions Between Arbuscular Mycorrhizal Fungi, Foliar Endophytic Fungi and Aphids – Nadia Ab Razak – Microbial Ecology

Other Microbes

Bacterial microcompartments for isethionate desulfonation in the taurine-degrading human-gut bacterium Bilophila wadsworthia – Anna G Burrichter – BMC Microbiology

Methods

Evaluation of Sample Preservation and Storage Methods for Metaproteomics Analysis of Intestinal Microbiomes – Angie Mordant – Microbiology Spectrum

Sample Processing for Metaproteomic Analysis of Human Gut Microbiota – Carmen García-Durán – Methods in Molecular Biology Enhancing Microbiome Research through Genome-Scale Metabolic Modeling – Nana Y D Ankrah – mSystems

December 4, 2021

Human and General Microbiome

Multivariate associative patterns between the gut microbiota and large-scale brain network connectivity – N Kohn – Gut Microbes

Cervicovaginal levels of human beta defensins during bacterial vaginosis – Nathalia Mayumi Noda-Nicolau – PloS ONE

Multiomics and digital monitoring during lifestyle changes reveal independent dimensions of human biology and health – Francesco Marabita – Cell Systems

A specific structure and high richness characterize intestinal microbiota of HIV-exposed seronegative individuals – Tulio J Lopera – PloS ONE

Central role of intestinal epithelial glucocorticoid receptor in alcohol- and corticosterone-induced gut permeability and systemic response – Pradeep K Shukla – The FASEB Journal

Proof-of-principle demonstration of endogenous circadian system and circadian misalignment effects on human oral microbiota – Sarah L Chellappa – The FASEB Journal

Gender Variations in the Oral Microbiomes of Elderly Patients with Initial Periodontitis – Jie Zhao – Journal of Immunology Research

Characterization of Esophageal Microbiota in Patients With Esophagitis and Esophageal Squamous Cell Carcinoma – Zongdan Jiang – Frontiers in Cellular and Infection Microbiology

Gender-Specific Differences in Gut Microbiota Composition Associated with Microbial Metabolites for Patients with Acne Vulgaris – Yukun Huang – Annals of Dermatology

Gut microbiota develop towards an adult profile in a sex-specific manner during puberty – Katri Korpela – Scientific Reports

Gut microbiota-driven brain Aβ amyloidosis in mice requires microglia – Hemraj B Dodiya – The Journal of Experimental Medicine

Associations of the oral microbiota and Candida with taste, smell, appetite and undernutrition in older adults – Kristina S Fluitman – Scientific Reports

Altered cervicovaginal microbiota in premenopausal ovarian cancer patients – Asuka Morikawa – Gene

Social overcrowding impacts gut microbiota, promoting stress, inflammation, and dysglycemia – Clara Delaroque – Gut Microbes

Research Highlight: Gut microbiome and autism spectrum disorder – Eleni Kotsiliti – Nature Reviews Gastroenterology & Hepatology

Human and General Microbiome (Reviews)

Metagenomics studies for the diagnosis and treatment of prostate cancer – Ali Zarei – The Prostate

Regulation of common neurological disorders by gut microbial metabolites – Jeongho Park – Experimental & Molecular Medicine

The gut microbiota in retinal diseases – Marie-Agnès Bringer – Experimental Eye Research

Microbe-based management for colorectal cancer – Zi-Yun Gao – Chinese Medical Journal

Novel Strategies for Inhibition of Bacterial Biofilm in Chronic Rhinosinusitis – Aref Shariati – Journal of Applied Microbiology

Regulation of para-cresol production in Clostridioides difficile – Mark A Harrison – Current Opinion in Microbiology

Animal Microbiome (Non-Models)

Gut microbiome and metabolome in a non-human primate model of chronic excessive alcohol drinking – Daria Piacentino – Translational Psychiatry

A holobiont view of island biogeography: unraveling patterns driving the nascent diversification of a Hawaiian spider and its microbial associates – Ellie E Armstrong – Molecular Ecology

Interactions of Muscovy duck reovirus, gut microbiota, and host innate immunity: Transcriptome and gut microbiota analysis – Zheng Zhu – Veterinary Microbiology

Antibiotics, antibiotic resistance genes and microbial community in grouper mariculture – Lu-Xi He – The Science of the Total Environment

Beneficial Microbes and Compounds

Lactobacillus alleviated obesity induced by high-fat diet in mice – Wei Song – Journal of Food Science

Effect of prophylactic dextrose gel on the neonatal gut microbiome – Sophie L St Clair – Archives of Disease in Childhood

Polydextrose with and without Bifidobacterium animalis ssp. lactis 420 drives the prevalence of Akkermansia and improves liver health in a multi-compartmental obesogenic mice study – Christian Clement Yde – PloS ONE

Review: Studies and Application of Sialylated Milk Components on Regulating Neonatal Gut Microbiota and Health – Yushuang Wang – Frontiers in Nutrition

Environmental Microbiome

The highly diverse Antarctic Peninsula soil microbiota as a source of novel resistance genes – Andrés E Marcoleta – The Science of the Total Environment

Other Microbiomes

In vitro interaction network of a synthetic gut bacterial community – Anna S Weiss – The ISME Journal

Plant and Fungi Microbiome

Tryptophan metabolism and bacterial commensals prevent fungal dysbiosis in Arabidopsis roots – Katarzyna W Wolinska – PNAS

An ancient antimicrobial protein co-opted by a fungal plant pathogen for in planta mycobiome manipulation – Nick C Snelders – PNAS

Seed inhabiting bacterial endophytes of maize promote seedling establishment and provide protection against fungal disease – Gaurav Pal – Microbiological Research

November 20, 2021

Highlights!

Review: Reporting guidelines for human microbiome research: the STORMS checklist – Chloe Mirzayi – Nature Medicine → The following article “provides guidance for concise and complete reporting of microbiome studies that will facilitate manuscript preparation, peer review, and reader comprehension of publications and comparative analysis of published results”

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Jiaqiang Wu – Microbiome → “Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference”

Metatranscriptomics to characterize respiratory virome, microbiome, and host response directly from clinical samples – Seesandra V Rajagopala – Cell Reports Methods → This study reports a method to study virome and microbiome of clinically relevant respiratory samples, using a children cohort. 

Human and General Microbiome

Response of Lung Microbiota to Changes of Pulmonary Innate Immunity Under Healthy Conditions – Taro Yasuma – American Journal of Respiratory and Critical Care Medicine

Small intestinal bacterial overgrowth in Alzheimer’s disease – Karol Kowalski – Journal of Neural Transmission 

Periodontitis Salivary Microbiota Worsens Colitis – J Qian – Journal of Dental Research

The Effects of Moderate Alcohol Consumption on Circulating Metabolites and Gut Microbiota in Patients With Coronary Artery Disease – Xinyue Zhao – Frontiers in Cardiovascular Medicine

Integrative Analysis of LGR5/6 Gene Variants, Gut Microbiota Composition and Osteoporosis Risk in Elderly Population – Dong-Sheng Di – Frontiers in Microbiology

Comparison of the Gut Microbiota in Patients with Benign and Malignant Breast Tumors: A Pilot Study – Peidong Yang – Evolutionary Bioinformatics Online

Temporal variability in quantitative human gut microbiome profiles and implications for clinical research – Doris Vandeputte – Nature Communications

Association between Parkinson’s disease and the faecal eukaryotic microbiota – Severin Weis – NPJ Parkinson’s Disease

Micronutrient supplements can promote disruptive protozoan and fungal communities in the developing infant gut – Ana Popovic – Nature Communications

An integrative understanding of the large metabolic shifts induced by antibiotics in critical illness – Andrea Marfil-Sánchez – Gut Microbes

Efficacy and Outcomes of Fecal Microbiota Transplantation for Recurrent Clostridioides difficile Infection in Children with Inflammatory Bowel Disease – Maribeth R Nicholson – Journal of Crohn’s & Colitis

The anti-inflammatory effect of bacterial short chain fatty acids is partially mediated by endocannabinoids – Amrita Vijay – Gut Microbes

Human and General Microbiome – Reviews

Bile acids as regulatory molecules and potential targets in metabolic diseases – Ai-Jin Xie – Life Sciences

Renaissance for Phage-Based Bacterial Control – Cory Schwarz – Environmental Science & Technology

Sulphur metabolism in colon cancer tissues: a case report and literature review – Hironori Fukuoka – The Journal of International Medical Research

Dietary fatty acids in gut health: Absorption, metabolism and function – E Xu – Animal Nutrition

The search for aliens within us: a review of evidence and theory regarding the foetal microbiome – Richard Cariño III – Critical Reviews in Microbiology

Human immune diversity: from evolution to modernity – Adrian Liston – Nature Immunology 

Beneficial Microbes and Compounds

Review: Human Milk Oligosaccharides as a Missing Piece in Combating Nutritional Issues during Exclusive Breastfeeding – Verawati Sudarma – Pediatric Gastroenterology, Hepatology & Nutrition

Review: Advancements in the Pharmaceutical Applications of Probiotics: Dosage Forms and Formulation Technology – Kshitis Chandra Baral – International Journal of Nanomedicine

Lactobacillus rhamnosus strain LRH05 intervention ameliorated body weight gain and adipose inflammation via modulating the gut microbiota in high-fat diet-induced obese mice – Yung-Tsung Chen – Molecular Nutrition & Food Research

Bifidobacterium infantis Maintains Genome Stability in Ulcerative Colitis via Regulating Anaphase-Promoting Complex Subunit 7 – Taotao Han – Frontiers in Microbiology

Galacto-oligosaccharide Supplementation Modulates Pathogen-Commensal Competition between Streptococcus agalactiae and Streptococcus salivarius – Rebecca E Moore – Chembiochem

Animal Microbiome (Non-models)

Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes – Yuqing Feng – Communications Biology

Contrasting microbiome dynamics of putative denitrifying bacteria in two octocoral species exposed to dissolved organic carbon (DOC) and warming – Nan Xiang – Applied and Environmental Microbiology

Plant Microbiome

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Nan Yang – NPJ Biofilms and Microbiomes

Drops join to make a stream: high-throughput nanoscale cultivation to grasp the lettuce root microbiome – Antoine Persyn – Environmental Microbiology Reports

Pan-genome analysis identifies intersecting roles for Pseudomonas specialized metabolites in potato pathogen inhibition – Alba Pacheco-Moreno – eLife

Small-scale agricultural grassland management can affect soil fungal community structure as much as continental scale geographic patterns – A Fox – FEMS Microbiology Ecology

Geographic and position-based variations in phyllospheric bacterial communities present on flue-cured tobacco – Jianbin Ye – Applied Microbiology and Biotechnology

Other Microbes

Improved quantitative microbiome profiling for environmental antibiotic resistance surveillance – Amelie Ott – Environmental Microbiome

Sediment Microbiota in Response to Circuitry of Sediment Microbial Fuel Cells, Revealed by 16S rRNA Gene Amplicon Sequencing – Yasuyuki Takemura – Microbiology Resource Announcements

Bacterial response to spatial gradients of algal-derived nutrients in a porous microplate – Hyungseok Kim – The ISME Journal

Review: Microbial ecology of tourist Paleolithic caves – Zelia Bontemps – The Science of the Total Environment

Microbiome Analysis and Bioinformatics

Multivariate statistical monitoring system for microbial population dynamics – Koji Ishiya – Physical Biology

GMrepo v2: a curated human gut microbiome database with special focus on disease markers and cross-dataset comparison – Die Dai – Nucleic Acids Research

metaSNV v2: detection of SNVs and subspecies in prokaryotic metagenomes – Thea Van Rossum – Bioinformatics

Assessing saliva microbiome collection and processing methods – Abigail J S Armstrong – NPJ Biofilms and Microbiomes

Analysing microbiome intervention design studies: Comparison of alternative multivariate statistical methods – Maryia Khomich – PloS ONE

Technical note: overcoming host contamination in bovine vaginal metagenomic samples with Nanopore adaptive sequencing – Chian Teng Ong – Journal of Animal Science

Mian: Interactive Web-Based Microbiome Data Table Visualization and Machine Learning Platform – Boyang Tom Jin – Bioinformatics

November 13, 2021

Human and General Microbiome

Visualized analysis of trends and hotspots in global oral microbiome research: A bibliometric study – Ga Liao – MedComm

A low abundance of genus Bacteroides in gut microbiota is negatively correlated with blood phenylalanine levels in Uygur patients with phenylketonuria – Yajie Su – Translational Pediatrics

Haematopoietic cell transplantation outcomes are linked to intestinal mycobiota dynamics and an expansion of Candida parapsilosis complex species – Thierry Rolling – Nature Microbiology

The composition of lung microbiome in lung cancer: a systematic review and meta-analysis – Sadaf Najafi – BMC Microbiology

A metaproteomic-based gut microbiota profiling in children affected by autism spectrum disorders – Stefano Levi Mortera – Journal of Proteomics

Is there an association between the vaginal microbiome and first trimester miscarriage? A prospective observational study – Monica Shahid – The Journal of Obstetrics and Gynaecology Research

Human and General Microbiome – Reviews

Review: Gut microbiota and vitamin status in persons with obesity: A key interplay – Lise Voland – Obesity Reviews

Review: Insights into the role of vaginal microbiome in women’s health – Namrata Deka – Journal of Basic Microbiology

Review: The gut virome in inflammatory bowel diseases – Guanxiang Liang – Current Opinion in Virology

Beneficial Microbiome and Compounds

Tuber flours improve intestinal health and modulate gut microbiota composition – Tao Xu – Food Chemistry: X

Effects of red ginseng on gut, microbiota, and brain in a mouse model of post-infectious irritable bowel syndrome – Seonhye Yu – Journal of Ginseng Research

Food Microbiome

The inconsistent microbiota of Budu, the Malaysian fermented anchovy sauce, revealed through 16S amplicon sequencing – Muhammad Zarul Hanifah Md Zoqratt – PeerJ

Animal Microbiome (non-models)

Seasonal diet and microbiome shifts in wild rhesus macaques are better correlated at the level of nutrient components than food items – Zhenwei Cui – Integrative Zoology

Wild gut microbiomes reveal individuals, species, and location as drivers of variation in two critically endangered Hawaiian honeycreepers – Maria S Costantini – PeerJ

Plant Microbiome

Opinion: The end of hunger: fertilizers, microbes and plant productivity – Hang-Wei Hu – Microbial Biotechnology

Enrichment of beneficial rhizosphere microbes in Chinese wheat yellow mosaic virus-resistant cultivars – Chuanfa Wu – Applied Microbiology and Biotechnology

Unexpected diversity among small-scale sample replicates of defined plant root compartments – Sally Attia – The ISME Journal

Microbiome analysis methods

Microbial enrichment and storage for metagenomics of vaginal, skin, and saliva samples – Sarah Ahannach – iScience

An integrated workflow for enhanced taxonomic and functional coverage of the mouse fecal metaproteome – Nicolas Nalpas – Gut Microbes

Improved Metabolite Prediction Using Microbiome Data-Based Elastic Net Models – Jialiu Xie – Frontiers in Cellular and Infection Microbiology

OtherEvaluation of Effects of Laboratory Disinfectants on Mouse Gut Microbiota – Joseph D Sciurba – Comparative Medicine

November 9, 2021

Human and General Microbiome

Bacteroides vulgatus and Bacteroides dorei predict immune-related adverse events in immune checkpoint blockade treatment of metastatic melanoma – Mykhaylo Usyk – Genome Medicine

A Genome-Phenome Association study in native microbiomes identifies a mechanism for cytosine modification in DNA and RNA – Weiwei Yang – eLife

The Gut Microbiome Modifies the Association between a Mediterranean Diet and Diabetes in US Hispanic / Latino Population – Dong D Wang – The Journal of Clinical Endocrinology and Metabolism

Proteomics analysis of the gut-brain axis in a gut microbiota-dysbiosis model of depression – Yiyun Liu – Translational Psychiatry

The Capacity to Produce Hydrogen Sulfide (H(2)S) via Cysteine Degradation Is Ubiquitous in the Human Gut Microbiome – Domenick J Braccia – Frontiers in Microbiology

Identification of a novel cancer microbiome signature for predicting prognosis of human breast cancer patients – A W Mao – Clinical & Translational Oncology

Gut microbiota of adults with asthma is broadly similar to non-asthmatics in a large population with varied ethnic origins – Robert F J Kullberg – Gut Microbes

Effects of fecal microbiota transplant on DNA methylation in subjects with metabolic syndrome – Eduard W J van der Vossen – Gut Microbes

The Mucosally-Adherent Rectal Microbiota Contains Features Unique to Alcohol-Related Cirrhosis – Ting-Chin David Shen – Gut Microbes

Multiple bacterial virulence factors focused on adherence and biofilm formation associate with outcomes in cirrhosis – Jasmohan S Bajaj – Gut Microbes

Long-term dynamics of the human oral microbiome during clinical disease progression – Ana Duran-Pinedo – BMC Biology

Microbiome characteristics and the key biochemical reactions identified on stone world cultural heritage under different climate conditions – Xinghua Ding – Journal of Environmental Management

Fecal biomarkers of environmental enteric dysfunction and the gut microbiota of rural Malawian children: An observational study – David Chaima – Heliyon

Review: The Evolving Role of Consensus Molecular Subtypes: a Step Beyond Inpatient Selection for Treatment of Colorectal Cancer – Javier Ros – Current Treatment Options in Oncology

Review: The role of the host microbiome in autism and neurodegenerative disorders and effect of epigenetic procedures in the brain functions – Bahman Yousefi – Neuroscience and Biobehavioral Reviews

Review: The Oral Microbiota and its Role in Carcinogenesis – Mark Stasiewicz – Seminars in Cancer Biology

Review: Gut microbiota: sculptors of the intestinal stem cell niche in health and inflammatory bowel disease – Manasvini Markandey – Gut Microbes

Review: The gastrointestinal microbiota in colorectal cancer cell migration and invasion – Charlotte Henstra – Clinical & Experimental Metastasis

Review: Akkermansia muciniphila and host interaction within the intestinal tract – Andrei M Karamzin – Anaerobe

Review: Effects of anti-aging interventions on intestinal microbiota – Yanjiao Du – Gut Microbes

Review: Impact of the environment on the microbiome – Herberto José Chong Neto – Jornal de Pediatria

Review: Progress and prospects of the healthy human gut virome – Stephen R Stockdale – Current Opinion in Virology

Forensic Microbiome

Review: Integrating the human microbiome in the forensic toolkit: Current bottlenecks and future solutions – Celia Díez López – Forensic Science International. Genetics

Beneficial Microbes, Compounds and Interventions

Bioactives and their metabolites from Tetrastigma hemsleyanum leaves ameliorate DSS-induced colitis via protecting the intestinal barrier, mitigating oxidative stress and regulating the gut microbiota – Tong Wu – Food & Function

Bacterial membrane vesicles and phages in blood after consumption of Lacticaseibacillus rhamnosus JB-1 – Kevin Champagne-Jorgensen – Gut Microbes

β-Glucan-triggered Akkermansia muciniphila expansion facilitates the expulsion of intestinal helminth via TLR2 in mice – Xuemin Jin – Carbohydrate Polymers

Review: The impact of a low-calorie, low-glycemic diet on systemic lupus erythematosus: a systematic review – Aline Mizusaki Imoto – Advances in Rheumatology

Review: Recent advances in the concept of paraprobiotics: Nutraceutical/functional properties for promoting children health – Harsh Kumar – Critical Reviews in Food Science and Nutrition

Review: Breastfeeding Contributes to Physiological Immune Programming in the Newborn – Alberto Camacho-Morales – Frontiers in Pediatrics

Animal Model Microbiome

Electroacupuncture could balance the gut microbiota and improve the learning and memory abilities of Alzheimer’s disease animal model – Jing Jiang – PloS ONE

Protective Effects of Bacillus amyloliquefaciens 40 Against Clostridium perfringens Infection in Mice – Zipeng Jiang – Frontiers in Nutrition

Animal Microbiome (non-models)

Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate – B Karina Montero – PLoS Pathogens

Metagenomic and network analysis revealed wide distribution of antibiotic resistance genes in monkey gut microbiota – Yueyang Yan – Microbiological Research

Comparative Study of the Gut Microbiota Among Four Different Marine Mammals in an Aquarium – Shijie Bai – Frontiers in Microbiology

Bacterial Communities of Lab and Field Northern House Mosquitoes (Diptera: Culicidae) Throughout Diapause – Elise M Didion – Journal of Medical Entomology

Gut Microbiome of Wild Baltic Salmon (Salmo salar L.) Parr – Vesta Skrodenytė-Arbačiauskienė – Microbial Ecology

Concerted impacts of antiherbivore defenses and opportunistic Serratia pathogens on the fall armyworm (Spodoptera frugiperda) – Charles J Mason – Oecologia

Plant Microbiome

Review: Sculpting the soil microbiota – Valéria Custódio – The Plant Journal

Extremophiles

Review: Microbial diversity in extreme environments – Wen-Sheng Shu – Nature Reviews Microbiology

Preprint: A large-scale genome-based survey of acidophilic Bacteria suggests that genome streamlining is an adaption for life at low pH – Diego Nahuel Cortez – BioRxiv

Other Microbes

Bacterial Community Structure and Metabolic Function Succession During the Composting of Distilled Grain Waste – Shi-Peng Wang – Applied Biochemistry and Biotechnology

Bioinformatics and Microbiome Analysis

AMDB: a database of animal gut microbial communities with manually curated metadata – Junwon Yang – Nucleic Acids Research

RESCRIPt: Reproducible sequence taxonomy reference database management – Michael S 2nd Robeson – PLoS Computational Biology

Reprocessing 16S rRNA Gene Amplicon Sequencing Studies: (Meta)Data Issues, Robustness, and Reproducibility – Xiongbin Kang – Frontiers in Cellular and Infection Microbiology

November 6, 2021

Have a nice weekend! Today we have a good variety of papers, in several different topics. Enjoy!

Human and General Microbiome

Metataxonomic investigation of the microbial community in the trachea and oropharynx of healthy controls and diabetic patients using endotracheal tubes – Sun Young Cho – PloS ONE

Characterization of the endometrial, cervicovaginal and anorectal microbiota in post-menopausal women with endometrioid and serous endometrial cancers – Gregory M Gressel – PloS ONE

Fecal Microbiota Transplantation Relieves Gastrointestinal and Autism Symptoms by Improving the Gut Microbiota in an Open-Label Study – Ning Li – Frontiers in Cellular and Infection Microbiology

Evaluation of vaginal microbiota in women admitted to the hospital for premature labour – Bruno Arena – Acta Bio-medica

The vaginal microbiota and innate immunity after local excisional treatment for cervical intraepithelial neoplasia – Anita Mitra – Genome Medicine

Comparative analysis of human facial skin microbiome between topical sites compared to entire face – Haeun Lee – Genes & Genomics

Lung Tissue Microbiome Is Associated With Clinical Outcomes of Idiopathic Pulmonary Fibrosis – Hee-Young Yoon – Frontiers in Medicine

Mechanisms underlying interactions between two abundant oral commensal bacteria – Dasith Perera – The ISME Journal

Epigenetic adaptations of the masticatory mucosa to periodontal inflammation – Gesa M Richter – Clinical Epigenetics

Increase of SARS-CoV-2 RNA load in faecal samples prompts for rethinking of SARS-CoV-2 biology and COVID-19 epidemiology – Mauro Petrillo – F1000Research

Microbiota-derived acetate enables the metabolic fitness of the brain innate immune system during health and disease – Daniel Erny – Cell Metabolism

Phage-delivered CRISPR-Cas9 for strain-specific depletion and genomic deletions in the gut microbiome – Kathy N Lam – Cell Reports

Cell-surface xyloglucan recognition and hydrolysis by the human gut commensal Bacteroides uniformis – Julie M Grondin – Applied and Environmental Microbiology

Dysbiosis of Gut Microbiome Is Associated With Rupture of Cerebral Aneurysms – Shuhei Kawabata – Stroke

Effect of Long-Term and Short-Term Imbalanced Zn Manipulation on Gut Microbiota and Screening for Microbial Markers Sensitive to Zinc Status – Lingjun Chen – Microbiology Spectrum

Dietary Modulation Alters Susceptibility to Listeria monocytogenes and Salmonella Typhimurium with or without a Gut Microbiota – Mathis Wolter – mSystems

Alterations in Gut Microbiome Composition and Function in Irritable Bowel Syndrome and Increased Probiotic Abundance with Daily Supplementation – Joann Phan – mSystems

The Future Is Big-and Small: Remote Sensing Enables Cross-Scale Comparisons of Microbiome Dynamics and Ecological Consequences – Deanna S Beatty – mSystems

Comprehensive functional core microbiome comparison in genetically obese and lean hosts under the same environment – Marina Martínez-Álvaro – Communications Biology

Vescimonas gen. nov., Vescimonas coprocola sp. nov., Vescimonas fastidiosa sp. nov., Pusillimonas gen. nov. and Pusillimonas faecalis sp. nov. isolated from human faeces – Maki Kitahara – International Journal of Systematic and Evolutionary Microbiology

Human and General Microbiome – Reviews

Engineering temporal dynamics in microbial communities – Carlotta Ronda – Current Opinion in Microbiology

From a parts list to assembly instructions and an operating manual: how small host models can re-write microbiome theory – Nic M Vega – Current Opinion in Microbiology

Microbiota-derived extracellular vesicles in interkingdom communication in the gut – Natalia Díaz-Garrido – Journal of Extracellular Vesicles

Multiple roles of short-chain fatty acids in Alzheimer disease – Hui Chen – Nutrition 

Role of gut microbiota in functional constipation – Shengsheng Zhang – Gastroenterology Report

Gut Feelings: The Microbiota-Gut-Brain Axis on Steroids – Sik Yu So – American Journal of Physiology. Gastrointestinal and Liver Physiology

Urobiome: An outlook on the metagenome of urological diseases – Rachel Shoemaker – Investigative and Clinical Urology

Animal Models

Utilizing a reductionist model to study host-microbe interactions in intestinal inflammation – Amy M Tsou – Microbiome

Disruption of autophagy by increased 5-HT alters gut microbiota and enhances susceptibility to experimental colitis and Crohn’s disease – Sabah Haq – Science Advances

Differences in the gut microbiota composition of rats fed with soybean protein and their derived peptides – Wenhui Li – Journal of Food Science

Animal Microbiome (non-model)

Unraveling differences in fecal microbiota stability in mammals: from high variable carnivores and consistently stable herbivores – Franziska Zoelzer – Animal Microbiome

The Role Transition of Dietary Species Richness in Modulating the Gut Microbial Assembly and Postweaning Performance of a Generalist Herbivore – Guoliang Li – mSystems

Age Associated Microbiome and Microbial Metabolites Modulation and Its Association With Systemic Inflammation in a Rhesus Macaque Model – Suresh Pallikkuth – Frontiers in Immunology

Strain-level analysis reveals the vertical microbial transmission during the life cycle of bumblebee – Qinzhi Su – Microbiome

Social convergence of gut microbiomes in vampire bats – Karthik Yarlagadda – Biology Letters

Shrimp AHPND Causing Vibrio anguillarum Infection: Quantitative Diagnosis and Identifying Antagonistic Bacteria – Huiyu Shen – Marine Biotechnology

Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition – C E Dubé – Nature Communications

Dry and Rainy Seasons Significantly Alter the Gut Microbiome Composition and Reveal a Key Enterococcus sp. (Lactobacillales: Enterococcaceae) Core Component in Spodoptera frugiperda (Lepidoptera: Noctuidae) Corn Strain From Northwestern Colombia – Marlon Felipe Higuita Palacio – Journal of Insect Science

Invasive Amphibian Gut Microbiota and Functions Shift Differentially in an Expanding Population but Remain Conserved Across Established Populations – Carla Wagener – Microbial Ecology

Review: Microbiome Studies in Non-human Primates – Jason M Brenchley – Current HIV/AIDS Reports

Beneficial Microbes and Compounds

Regulation divergences of Lactobacillus fermentum PCC and Lactobacillus paracasei 431 on penicillin-induced upper respiratory tract microbial dysbiosis in BALB/c mice – Feng Gao – Food & Function

Dietary calcium phosphate strongly impacts gut microbiome changes elicited by inulin and galacto-oligosaccharides consumption – Jori Fuhren – Microbiome

Plant Microbiome

Effects of growth promoting microorganisms on tomato seedlings growing in different media conditions – Robert Pokluda – PloS ONE

Inter-Kingdom Networks of Canola Microbiome Reveal Bradyrhizobium as Keystone Species and Underline the Importance of Bulk Soil in Microbial Studies to Enhance Canola Production – Jean-Baptiste Floc’h – Microbial Ecology

Built Environment Microbiome

City-Scale Meta-Analysis of Indoor Airborne Microbiota Reveals that Taxonomic and Functional Compositions Vary with Building Types – You Zhou – Environmental Science & Technology

Environmental Microbiome

Heavy metals and microbiome are negligible drivers than mobile genetic elements in determining particle-attached and free-living resistomes in the Yellow River – Qiaoling Yu – Journal of Hazardous Materials

Forensic Microbiome

Assessment of the link between evidence and crime scene through soil bacterial and fungal microbiome: A mock case in forensic study – Sukriye Karadayı – Forensic Science International

Microbiome Analysis Methods; Bioinformatics 

Bakta: rapid and standardized annotation of bacterial genomes via alignment-free sequence identification – Oliver Schwengers – Microbial Genomics

Compositional Data Analysis of Microbiome and Any-Omics Datasets: A Validation of the Additive Logratio Transformation – Michael Greenacre – Frontiers in Microbiology

Machine Learning Based Metagenomic Prediction of Inflammatory Bowel Disease – Andrea Mihajlović – Studies in Health Technology and Informatics

Evaluating de Novo Assembly and Binning Strategies for Time Series Drinking Water Metagenomes – Solize Vosloo – Microbiology Spectrum

Evaluation of the effect of antibiotics on gut microbiota in early life based on culturomics, SMRT sequencing and metagenomics sequencing methods – Lihan Wang – Analytical Methods