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

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

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

Highlights!

Intestinal Bacteriophage Therapy: Looking for Optimal Efficacy – François Javaudin – Clinical Microbiology Reviews → in this review, authors discuss different aspects of the applications of bacteriophage therapy in mammals.

Wildlife symbiotic bacteria are indicators of the health status of the host and its ecosystem – Maria Bravo – Applied and Environmental Microbiology → This study highlights the role of lactic acid bacteria as an useful indicator of wildlife health status. 

High-coverage metabolomics uncovers microbiota-driven biochemical landscape of interorgan transport and gut-brain communication in mice – Yunjia Lai – Nature Communications → in this report, profile from stool, blood and brain samples were obtained comparing germ-free and conventional mice, in order to gain more insight about the microbiota-gut-brain axis.

Human and General Microbiome

Analysis of gut microbiota and metabolites in patients with rheumatoid arthritis and identification of potential biomarkers – Yumei Chen – Aging

Gut-microbiota-microglia-brain interactions in Alzheimer’s disease: knowledge-based, multi-dimensional characterization – QuanQiu Wang – Alzheimer’s Research & Therapy

Alterations in the oral microbiome in HIV infection: causes, effects and potential interventions – Shuang Li – Chinese Medical Journal

Utilization efficiency of human milk oligosaccharides by human-associated Akkermansia is strain-dependent – Estefani Luna – Applied and Environmental Microbiology

Upper Respiratory Tract Microbiome of Australian Aboriginal and Torres Strait Islander Children in Ear and Nose Health and Disease – Andrea Coleman – Microbiology Spectrum

Review: The Human Microbiome in immunobullous disorders and lichen planus – M Karimova – Clinical and Experimental Dermatology

Beneficial Microbes and Compounds

Review: What is unknown in using Microbiota as a Therapeutic? – Joseph Jy Sung – Journal of Gastroenterology and Hepatology

Isolation and Identification of Potential Probiotic Bacteria from Human Milk – Quésia S Damaceno – Probiotics and Antimicrobial Proteins

Probiotics as the live microscopic fighters against Helicobacter pylori gastric infections – Masoud Keikha – BMC Gastroenterology

The probiotic Companilactobacillus crustorum MN047 alleviates colitis-associated tumorigenesis via modulating the intestinal microenvironment – Tao Wang – Food & Function

Lactobacillus rhamnosus and Bifidobacterium longum alleviate colitis and cognitive impairment in mice by regulating IFN-γ to IL-10 and TNF-α to IL-10 expression ratios – Xiaoyang Ma – Scientific Reports

Review: Interaction between four galactans with different structural characteristics and gut microbiota – Song Li – Critical Reviews in Food Science and Nutrition

Non-Model Animal Microbiome

Habitat Disturbance Linked with Host Microbiome Dispersion and Bd Dynamics in Temperate Amphibians – Wesley J Neely – Microbial Ecology

The Microbial Composition of Penaeid Shrimps’ Hepatopancreas Is Modulated by Hemocyanin – Zhihong Zheng – Journal of Immunology

Overabundance of Asaia and Serratia Bacteria Is Associated with Deltamethrin Insecticide Susceptibility in Anopheles coluzzii from Agboville, Côte d’Ivoire – Bethanie Pelloquin – Microbiology Spectrum

Genomics and phylogeny of the proposed phylum ‘Candidatus Poribacteria’ associated with the excavating sponge Thoosa mismalolli – Adrián González-Castillo – Antonie van Leeuwenhoek

Plant Microbiome

Microbial Diversity in Cultivated and Feral Vanilla Vanilla planifolia Orchids Affected by Stem and Rot Disease – Ireri A Carbajal-Valenzuela – Microbial Ecology

Indirect reduction of Ralstonia solanacearum via pathogen helper inhibition – Mei Li – The ISME Journal

Comparative Analysis of the Cultured and Total Bacterial Community in the Wheat Rhizosphere Microbiome Using Culture-Dependent and Culture-Independent Approaches – Sameh H Youseif – Microbiology Spectrum

Other Microbes

Mechanistic Insight into Yeast Bloom in a Lactic Acid Bacteria Relaying-Community in the Start of Sourdough Microbiota Evolution – Mugihito Oshiro – Microbiology Spectrum

Highlights!

Parallelism of intestinal secretory IgA shapes functional microbial fitness – Tim Rollenske – Nature → By using recombinant IgAs, researchers showed that IgA may shape the metabolism of intestinal bacteria, and in some cases IgA molecules against a same target have a different effect on the activity.

Hallstatt miners consumed blue cheese and beer during the Iron Age and retained a non-Westernized gut microbiome until the Baroque period – Frank Maixner – Current Biology → From the analysis of paleofeces, researchers suggest that people from the Austrian zone of Hallstatt could retain a non-westernized diet for centuries; in some cases, a high consumption of blue cheese and beer is suggested by the detection of Penicillium roqueforti and Saccharomyces cerevisiae DNA in the samples.  

In vitro study of the effect of quinoa and quinoa polysaccharides on human gut microbiota – Hitache Zeyneb – Food Science & Nutrition → quinoa, a very nutritious Andean cereal,  contains polysaccharides with potential prebiotic (health-promoting) properties.

Metagenomic analysis of gut microbiome reveals a dynamic change in Alistipes onderdonkii in the preclinical model of pancreatic cancer, suppressing its  proliferation – Kihak Lee – Applied Genetics and Molecular Biotechnology → RNA-seq analysis in a preclinical model revealed that the A. onderdonkii medium induced unique transcriptomic alterations in the pancreatic cancer cells, suggesting an special role in this disease.

Human and General Microbiome

Review: Biomarkers of geroprotection and cardiovascular health: An overview of omics studies and established clinical biomarkers in the context of diet – Riccardo Secci – Critical Reviews in Food Science and Nutrition

Unravelling the collateral damage of antibiotics on gut bacteria – Lisa Maier – Nature

Direct on-swab metabolic profiling of vaginal microbiome host interactions during pregnancy and preterm birth – Pamela Pruski – Nature Communications

Brain development in premature infants: A bug in the programming system? – Gerard Clarke – Cell Host & Microbe

A colon cancer prequel – John T Wren – Cell Host & Microbe

Metagenomic Analysis of Saliva Reveals Disease-Associated Microbiotas in Patients With Periodontitis and Crohn’s Disease-Associated Periodontitis – Boyang Sun – Frontiers in Cellular and Infection Microbiology

Antibiotic use but not gastrointestinal infection frequently precedes first diagnosis of functional gastrointestinal disorders – Michael P Jones – United European Gastroenterology Journal

Impact of Helicobacter pylori eradication on the gastric microbiome – Li-Qi Mao – Gut Pathogens

Baseline co-medications may alter the anti-tumoural effect of checkpoint inhibitors as well as the risk of immune-related adverse events – Marie Kostine – European Journal of Cancer

Cultivation of common bacterial species and strains from human skin, oral, and gut microbiota – Elizabeth Fleming – BMC Microbiology

Effect of chewing betel nut on the gut microbiota of Hainanese – Li Ying – PloS ONE

Animal Models

Transplantation of fecal microbiota from patients with inflammatory bowel disease and depression alters immune response and behavior in recipient mice – Hyo-Min Jang – Scientific Reports

Temporal relationship between alterations in the gut microbiome and the development of polycystic ovary syndrome-like phenotypes in prenatally androgenized female mice – Akari Kusamoto – The FASEB Journal

Gut microbiota dysbiosis of type 2 diabetic mice impairs the intestinal daily rhythms of GLP-1 sensitivity – Estelle Grasset – Acta Diabetologica

Non-Model Animal Microbiome

Diurnal oscillations in gut bacterial load and composition eclipse seasonal and lifetime dynamics in wild meerkats – Alice Risely – Nature Communications

Diet diversity and environment determine the intestinal microbiome and bacterial pathogen load of fire salamanders – Yu Wang – Scientific Reports

The structure of the cereal leaf beetle (Oulema melanopus) microbiome depends on the insect’s developmental stage, host plant, and origin – Beata Wielkopolan – Scientific Reports

Beneficial Microbes and Compounds

Review: Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Yue Han – Current Opinion in Pharmacology

Characterization of a new bacteriocin-like inhibitory peptide produced by Lactobacillus sakei B-RKM 0559 – Gulyaim K Abitayeva – Biotechnology Letters

Probiotic Interventions Alleviate Food Allergy Symptoms Correlated With Cesarean Section: A Murine Model – Bi-Ying Jin – Frontiers in Immunology

Selenium-enriched Bifidobacterium longum DD98 attenuates irinotecan-induced intestinal and hepatic toxicity in vitro and in vivo – Hui Zhu – Biomedicine & Pharmacotherapy

Phages

Novel lytic bacteriophage vB_GEC_EfS_9 against Enterococcus faecium – S Rigvava – Virus Research

Environmental Microbiome

Charting the complexity of the activated sludge microbiome through a hybrid sequencing strategy – Lei Liu – Microbiome

Other

PBK model-based prediction of intestinal microbial and host metabolism of zearalenone and consequences for its estrogenicity – Diana M Mendez-Catala – Molecular Nutrition & Food Research

Highlights!

Commensal microbiota divergently affect myeloid subsets in the mammalian central nervous system during homeostasis and disease – Roman Sankowski – The EMBO Journal → This study shows how perturbations in the microbiota drive changes in gene expression profiles in the CNS-associated macrophages, with concomitant effects on the  CNS myeloid cells, including Alzheimer-associated repercussions in a specialized murine model.

Coordination of root auxin with the fungus Piriformospora indica and bacterium Bacillus cereus enhances rice rhizosheath formation under soil drying – Feiyun Xu – The ISME Journal → In this study, authors report a cooperative effect of an endophytic fungus and a plant growth-promoting bacterium in rhizosheath formation when moderate soil drying, an agricultural technique used to improve water utilization, is performed.

Human and General Microbiome

Review: The role of Akkermansia muciniphila in obesity, diabetes and atherosclerosis – Alka Hasani – Journal of Medical Microbiology

Review: How can probiotic improve irritable bowel syndrome symptoms? – Indira Benjak Horvat – World Journal of Gastrointestinal Surgery

Meta-Analysis of the Composition of Human Intestinal Gases – Andre Modesto – Digestive Diseases and Sciences

Effectiveness of Probiotics and Prebiotics Against Acute Liver Injury: A Meta-Analysis – Sheng Xu – Frontiers in Medicine

The bacterial gut microbiome of probiotic-treated very-preterm infants: changes from admission to discharge – Jacob A F Westaway – Pediatric Research

Discovery of β-N-acetylglucosaminidases from screening metagenomic libraries and their use as thioglycoligase mutants – Gregor Tegl – Organic & Biomolecular Chemistry

Animal Microbiome

Comparing the gut microbiome along the gastrointestinal tract of three sympatric species of wild rodents – Jason L Anders – Scientific Reports

Changes in rumen microbial community composition in yak in response to seasonal variations – Xiaodan Huang – Journal of Applied Microbiology

Faecalicatena faecalis sp. nov., a moderately alkaliphilic bacterial strain isolated from swine faeces – Byeong Seob Oh – Antonie van Leeuwenhoek

Plant Microbiome

Capacity of soil bacteria to reach the phyllosphere and convergence of floral communities despite soil microbiota variation – Julien Massoni –  PNAS

Distinct Endophytic Bacterial Communities Inhabiting Seagrass Seeds – Flavia Tarquinio – Frontiers in Microbiology

Fungi Microbiome

Widespread bacterial diversity within the bacteriome of fungi – Aaron J Robinson – Communications Biology

Environmental Microbiome

Preprint: Genomic and metabolic adaptations of biofilms to ecological windows of opportunities in glacier-fed streams – Susheel Bhanu Busi – Biorxiv

Highlights!

Review: Bacterial Translocation as Inflammatory Driver in Crohn’s Disease – Raquel Linares – Frontiers in Cell and Developmental Biology

Review:  The Gut Microbiome and Inflammatory Bowel Diseases – Yue Shan – Annual Review of Medicine

Vegan vs. omnivore diets paradox: A whole-metagenomic approach for defining metabolic networks during the race in ultra-marathoners- a before and after study  design – Aslı Devrim-Lanpir – PloS ONE

The Prebiotic Potential of Inulin-type Fructans: A Systematic Review – Riley L Hughes – Advances in Nutrition

Next-generation prebiotic promotes selective growth of bifidobacteria, suppressing Clostridioides difficile – Rika Hirano – Gut Microbes

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols

Human and General Microbiome

Persistence of functional microbiota composition across generations – Christian Ramos – Scientific Reports

Gastric microbiota in patients with Helicobacter pylori-negative gastric MALT lymphoma. – Takahide Tanaka – Medicine

Lachnospira is a signature of antihistamine efficacy in chronic spontaneous urticarial – Runqiu Liu – Experimental Dermatology

Association of Female Genital Schistosomiasis With the Cervicovaginal Microbiota and Sexually Transmitted Infections in Zambian Women – Amy S Sturt – Open Forum Infectious Diseases

Gut Lactobacillus Level Is a Predictive Marker for Coronary Atherosclerotic Lesions Progress and Prognosis in Patients With Acute Coronary Syndrome – Jing Gao – Frontiers in Cellular and Infection Microbiology

Causal Effects of Gut Microbiome on Systemic Lupus Erythematosus: A Two-Sample Mendelian Randomization Study – Kun Xiang – Frontiers in Immunology

Vaginal microbiome as a tool for prediction of chorioamnionitis in preterm labor: a pilot study – Daichi Urushiyama – Scientific Reports

Genital mycoplasma infection and spontaneous preterm birth outcome: a prospective cohort study. – Giulia Karnauchovas Porto Cunha – BJOG

Endometrial microbiota is more diverse in people with endometriosis than symptomatic controls – Jocelyn M Wessels – Scientific Reports

Periodontitis associates with species-specific gene expression of the oral microbiota – Daniel Belstrøm – NPJ biofilms and microbiomes

Review: Interplay and cooperation of Helicobacter pylori and gut microbiota in gastric carcinogenesis – Seyedeh Zahra Bakhti – BMC Microbiology

Comparative Analyses of the Transport Proteins Encoded within the Genomes of nine Bifidobacterium Species – Hassan Zafar – Microbial Physiology

Review: Mass spectrometry-based metabolomics in microbiome investigations – Anelize Bauermeister – Nature Reviews Microbiology

Gut microbiota depletion exacerbates cholestatic liver injury via loss of FXR signalling – Kai Markus Schneider – Nature Metabolism

Review: Chains of evidence from correlations to causal molecules in microbiome-linked diseases. – Snehal N Chaudhari – Nature Chemical Biology

Review: Host and microbiota metabolic signals in aging and longevity – Yue Zhou – Nature Chemical Biology

Fecal filtrate transplantation protects against necrotizing enterocolitis – Anders Brunse – The ISME Journal

High-fat diet increases the severity of Giardia infection in association with low-grade inflammation and gut microbiota dysbiosis – Thibault Allain – Scientific Reports

Beneficial Microbes and Compounds

Effects of konjac glucomannan with different molecular weights on gut microflora with antibiotic perturbance in in-vitro fecal fermentation – Yu-Heng Mao – Carbohydrate Polymers

Review: Interactions between dietary polyphenols and aging gut microbiota: A review – Sergio Davinelli – BioFactors

Safety and efficacy of using heat-killed Lactobacillus plantarum L-137: High-dose and long-term use effects on immune-related safety and intestinal bacterial flora – Hiroko Nakai – Journal of Immunotoxicology

Faecalibacterium prausnitzii Attenuates DSS-Induced Colitis by Inhibiting the Colonization and Pathogenicity of Candida albicans – Xiaqiong Mao – Molecular Nutrition & Food Research

Minireview: Probiotics, Prebiotics, and Synbiotics for the Prevention of Necrotizing Enterocolitis. – Kiera Murphy – Frontiers in Nutrition

Review: Main drivers of (poly)phenol effects on human health: metabolite production and/or gut microbiota-associated metabotypes? – Carlos E Iglesias-Aguirre – Food & Function

Inhibitory effects of Lactobacillus casei Shirota against both Candida auris and Candida spp. isolates that cause vulvovaginal candidiasis and are resistant to antifungals – Aline Lorenzoni Paniágua – BMC Complementary Medicine and Therapies

Fructooligosaccharides: From Breast Milk Components to Potential Supplements. A Systematic Review– Valentina De Cosmi – Advances in Nutrition

Effects of Microbiota-Driven Therapy on Circulating Trimethylamine-N-Oxide Metabolism: A Systematic Review and Meta-Analysis – Lina Miao – Frontiers in Cardiovascular Medicine

Animal Microbiome

The spleen bacteriome of wild rodents and shrews from Marigat, Baringo County, Kenya. – Rehema Liyai – PeerJ

Marked Seasonal Variation in Structure and Function of Gut Microbiota in Forest and Alpine Musk Deer – Feng Jiang – Frontiers in Microbiology

Social groups constrain the spatiotemporal dynamics of wild sifaka gut microbiomes – Amanda C Perofsky – Molecular Ecology

Association of female reproductive tract microbiota with egg production in layer chickens – Yuan Su – GigaScience

Plant Microbiome

Bacillus subtilis Colonization of Arabidopsis thaliana Roots Induces Multiple Biosynthetic Clusters for Antibiotic Production – Harsh Maan – Frontiers in Cellular and Infection Microbiology

Environmental Microbiome

Review: Prospects for multi-omics in the microbial ecology of water engineering – Elizabeth A McDaniel – Water Research

Bioinformatics

QSDB-a graphical Quorum Sensing Database – Karsten Klein – Database

Testing microbiome association using integrated quantile regression models – Tianying Wang – Bioinformatics 

timeOmics: an R package for longitudinal multi-omics data integration – Antoine Bodein – Bioinformatics 

Automation of QIIME2 Metagenomic Analysis Platform – Calvin Fung – Current Protocols