December 30, 2022

Happy New Year from the Microbiome Digest Team!

Human and General Microbiome

Microbiome Characteristics in Early Threatened Miscarriage Study (MCETMS): a study protocol for a prospective cohort investigation in China – Xiaofeng Chen – BMJ Open

Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health – Yuan Huang – Microbiome

Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut – Ran Li – Nature Communications

Fecal level of butyric acid, a microbiome-derived metabolite, is increased in patients with severe carotid atherosclerosis – Kristine Stø – Scientific Reports

Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women – Young-Ah You – Scientific Reports

Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study – Freida Blostein – Microbiome

Systematic Review: The effects of microbiota abundance on symptom severity in Parkinson’s disease: A systematic review – Eliša Papić – Frontiers in Aging Neuroscience

Systematic Review: A systematic review of microbiome-derived biomarkers for early colorectal cancer detection – Florine H Zwezerijnen-Jiwa – Neoplasia

Review: Current insights into skin lipids and their roles in cutaneous health and disease – Anna Nicolaou – Current Opinion in Clinical Nutrition and Metabolic Care

Beneficial Microbes and Compounds

Akkermansia supplementation reverses the tumor-promoting effect of the fecal microbiota transplantation in ovarian cancer – Zizhuo Wang – Cell Reports

Review: A novel approach to Lactiplantibacillus plantarum: From probiotic properties to the omics insights – Noemí Echegaray – Microbiological Research

Animal Microbiome

Prokaryotic and eukaryotic microbial communities associated with coral species have high host specificity in the South China Sea – Keke Cheng – The Science of the Total Environment

Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler – Sarah F Worsley – Microbiome

Gut microbe Lactiplantibacillus plantarum undergoes different evolutionary trajectories between insects and mammals – Elisa Maritan – BMC Biology

Environmental Microbiome

Permafrost in the Cretaceous supergreenhouse – Juan Pedro Rodríguez-López – Nature Communications

Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes – Thomas Grevesse – Microbiome

Temporary establishment of bacteria from indoor plant leaves and soil on human skin – Gwynne Á Mhuireach – Environmental Microbiome

Microbiome Analysis

Stochastic variational variable selection for high-dimensional microbiome data – Tung Dang – Microbiome

December 23, 2022

Happy Holidays from the Microbiome Digest Team!

Human and General Microbiome

Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the AMICA project – A Tramice – Scientific Reports

Diversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota – Disha Bhattacharjee – mSphere

A multiomics analysis of direct interkingdom dynamics between influenza A virus and Streptococcus pneumoniae uncovers host-independent changes to bacterial virulence fitness – Maryann P Platt – PLoS Pathogens

Butyrate Ameliorates Insufficient Sleep-Induced Intestinal Mucosal Damage in Humans and Mice – Ting Gao – Microbiology Spectrum

Prediction model of poorly differentiated colorectal cancer (CRC) based on gut bacteria – Zhang Qi – BMC Microbiology

Multidisciplinary Perinatal Care in IBD – Lihi Godny – Journal of Crohn’s & Colitis

Review: A multi-omic brain gut microbiome signature differs between IBS subjects with different bowel habits – Rachel P Sarnoff – Neuropharmacology

Review: From fecal microbiota transplantation toward next-generation beneficial microbes: The case of Anaerobutyricum soehngenii – Koen Wortelboer – Frontiers in Medicine

Beneficial Microbes and Compounds

Final Results from a Phase 2b Randomized, Placebo-Controlled Clinical Trial of RBX2660: A Microbiota-Based Drug for the Prevention of Recurrent Clostridioides difficile Infection – Erik R Dubberke – Infectious Diseases and Therapy

Systematic Review: The effect of probiotic and synbiotic supplementation on appetite-regulating hormones and desire to eat: a systematic review and meta-analysis of clinical trials – Morvarid Noormohammadi – Pharmacological Research

Animal Microbiome

Experimental Infection with Mycoplasma hyopneumoniae Strain 232 in Swine Influences the Lower Respiratory Microbiota – Henrique Meiroz de Souza Almeida – Veterinary Sciences

Functional Diversification of Oyster Big Defensins Generates Antimicrobial Specificity and Synergy against Members of the Microbiota – Noémie De San Nicolas – Marine Drugs

Gut microbiota modulates lung fibrosis severity following acute lung injury in mice – Ozioma S Chioma – Communications Biology

Effects of enhanced insect feeding on the faecal microbiota and transcriptome of a family of captive common marmosets (Callithrix jacchus) – Yumiko Yamazaki – PloS ONE

Review: The Mechanism of Important Components in Canine Fecal Microbiota Transplantation – Kerong Li – Veterinary Sciences

Food Microbiome

In vitro selection and characterization of probiotic properties in eight Lactobacillus strains isolated from cocoa fermentation – Milena E DE Almeida – Anais da Academia Brasileira de Ciencias

Microbiome Analysis Techniques

RIAM: A Universal Accessible Protocol for the Isolation of High Purity DNA from Various Soils and Other Humic Substances – Alexander G Pinaev – Methods and Protocols

Review: Compositionality, sparsity, spurious heterogeneity, and other data-driven challenges for machine learning algorithms within plant microbiome studies – Sebastiano Busato – Current Opinion in Plant Biology

December 19, 2022

Highlights!

Multi-omic interactions in the gut of children at the onset of islet autoimmunity – Patrick G Gavin – Microbiome

“Here, we apply an integrative approach to combine comprehensive fecal virome, microbiome, and metaproteome data sampled before and at the onset of islet autoimmunity in 40 children at increased risk of T1D […] We show a functional remodeling of the gut microbiota accompanies both islet autoimmunity and viral infection with a switch in function in Faecalibacterium occurring at the onset of islet autoimmunity.”

Human and General Microbiome

Review: The microbiota-gut-brain axis in pathogenesis of depression: a narrative review – Hui Yao – Physiology & Behavior

Review: Environmental enteric dysfunction: gut and microbiota adaptation in pregnancy and infancy – Carrie A Cowardin – Nature Reviews. Gastroenterology & Hepatology

Review: Gastrointestinal Tract, Microbiota and Multiple Sclerosis (MS) and the Link Between Gut Microbiota and CNS – Bahman Yousefi – Current Microbiology

Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort – Nele Brusselaers – Gut Pathogens

Endodontic microbial communities in apical periodontitis – Alessio Buonavoglia – Journal of Endodontics

Gut Microbiota-Generated Phenylacetylglutamine and Heart Failure – Kymberleigh A Romano – Circulation. Heart Failure

Animal Microbiome

Midgut Bacterial Microbiota of 12 Fish Species from a Marine Protected Area in the Aegean Sea (Greece) – Konstantinos Kormas – Microbial Ecology

Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host – Ankur Midha – Microbiome

Plant Microbiome

Multifaceted roles of flavonoids mediating plant-microbe interactions – Lanxiang Wang – Microbiome

Microbiome Analysis and Techniques

An economic and robust TMT labeling approach for high throughput proteomic and metaproteomic analysis – Marybeth Creskey – Proteomics

Machine learning-derived gut microbiome signature predicts fatty liver disease in the presence of insulin resistance – Baeki E Kang – Scientific Reports

Pseudomonas-specific 16S rRNA insect gut-microbiome profiling using next-generation sequencing – Ayushi Gupta – STAR Protocols

December 16, 2022

Highlights!

A microbiome-dependent gut-brain pathway regulates motivation for exercise – Lenka Dohnalová – Nature 

Here, we report on the discovery of a gut–brain connection in mice that enhances exercise performance by augmenting dopamine signalling during physical activity. We find that microbiome-dependent production of endocannabinoid metabolites in the gut stimulates the activity of TRPV1-expressing sensory neurons and thereby elevates dopamine levels in the ventral striatum during exercise.

Gut microbiota in the early stage of Crohn’s disease has unique characteristics – Xianzong Ma – Gut Pathogens

The present study aimed to identify dysbacteriosis in patients with early Crohn’s Disease (CD) and explore specific gut bacteria related to the progression of CD.

Human and General Microbiome

Longitudinal multi-omics analyses of the gut-liver axis reveals metabolic dysregulation in hepatitis C infection and cirrhosis – Rabab O Ali – Nature Microbiology

Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome – Pablo Villoslada-Blanco – Scientific Reports

Consequences of collagen induced inflammatory arthritis on circadian regulation of the gut microbiome – Devin Amanda Simpkins – FASEB Journal

Isolation and characterization of a novel choline degrading Citrobacter amalonaticus strain from the human gut – Jyoti Kashyap – Current Research in Microbial Sciences

HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome – Jingjing Meng – Microbiology Spectrum

Gut dysbiosis and bacterial translocation in the aneurysmal wall and blood in patients with abdominal aortic aneurysm – Ken Nakayama – PloS One

Review: Female reproductive tract microbiome and early miscarriages – Olga Lebedeva – APMIS

Review: Emerging roles of intratumor microbiota in cancer metastasis – Aikun Fu – Trends in Cell Biology

In Brief: Urine microbiota differ in bladder cancer – Louise Stone – Nature Reviews. Urology

Animal Microbiome

Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru – Jesús Rojas-Jaimes – BMC Microbiology

Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets – Guang Pu – mSystems

Review: Involvement of Microbiota in Insect Physiology: Focus on B Vitamins – Javier Serrato-Salas – mBio

Plant Microbiome

The Endophytic Root Microbiome Is Different in Healthy and Ralstonia solanacearum-Infected Plants and Is Regulated by a Consortium Containing Beneficial Endophytic Bacteria – Yiting Li – Microbiology Spectrum

Microbiome Analysis and Methods

Interpreting tree ensemble machine learning models with endoR – Albane Ruaud – PLoS Computational Biology

Analysis of Ancient Microbial DNA – Olivier Gorgé – Methods in Molecular Biology (Book)

Confocal Laser Scanning Microscopy Approach to Investigate Plant-Fungal Interactions – F Fracchia – Methods in Molecular Biology (Book)

December 2, 2022

Human and General Microbiome

Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis – Shuwen Han – Microbiology Spectrum

The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population – Wen Zhang – Microbiology Spectrum

The Gut Microbiota is Important for the Maintenance of Blood-Cerebrospinal Fluid Barrier Integrity – Emily G Knox – The European Journal of Neuroscience

Evaluation of co-circulating pathogens and microbiome from COVID-19 infections – James B Thissen – PloS One

A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics – Margot Delavy – mBio

Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species – Shushan Sargsian – Cell Reports

Genome Watch: Zooming into the structure of the microbiome – Gemma G R Murray – Nature Reviews. Microbiology

Beneficial Microbes and Compounds

Saussurea involucrata oral liquid regulates gut microbiota and serum metabolism during alleviation of collagen-induced arthritis in rats – Shan Cong – Phytotherapy Research

Prebiotic oligofructose protects against high-fat diet-induced obesity by changing the gut microbiota, intestinal mucus production, glycosylation and secretion – Paola Paone – Gut Microbes

Review: Predicting Personalized Responses to Dietary Fiber Interventions: Opportunities for Modulation of the Gut Microbiome to Improve Health – Car Reen Kok – Annual Review of Food Science and Technology

Animal Microbiome

Gut dysbiosis induces the development of mastitis through a reduction in host anti-inflammatory enzyme activity by endotoxemia – Caijun Zhao – Microbiome

Chronic clinical signs of upper respiratory tract disease associate with gut and respiratory microbiomes in a cohort of domestic felines – Holly Kristin Arnold – PloS One

Plant and Soil Microbiome

Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions – Zhonghua Wang – Microbiology Spectrum

Impacts of maize hybrids with different nitrogen use efficiency on root-associated microbiota based on distinct rhizosphere soil metabolites – Keke Li – Environmental Microbiology

Environmental Microbiome

Coupled C, H, N, S and Fe biogeochemical cycles operating in the continental deep subsurface of the Iberian Pyrite Belt – Ricardo Amils – Environmental Microbiology

Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes – N V Patin – mSystems

Bioinformatics and Microbiome Analysis

The Application of Spearman Partial Correlation for Screening Predictors of Weight Loss in a Multiomics Dataset – Joel Correa da Rosa – Omics

Sampling of Human Microbiomes to Screen for Antibiotic-Producing Commensals – Benjamin Torres Salazar – Methods in Molecular Biology

September 24, 2022

Human and General Microbiome

Systemic antibody responses against human microbiota flagellins are overrepresented in chronic fatigue syndrome patients – Thomas Vogl – Science Advances

Strain-level resolution and pneumococcal carriage dynamics by single-molecule real-time (SMRT) sequencing of the plyNCR marker: a longitudinal study in Swiss infants – Oluwaseun Rume-Abiola Oyewole – Microbiome

Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis – Victoria M Martin – Microbiome

Host and gut bacteria share metabolic pathways for anti-cancer drug metabolism – Peter Spanogiannopoulos – Nature Microbiology

Diet-driven microbial ecology underpins associations between cancer immunotherapy outcomes and the gut microbiome – Rebecca C Simpson – Nature Medicine

Advances in the gut microbiome and mood disorders – Sabrina Mörkl – Current Opinion in Psychiatry

Review: Modulation of the intestinal microbiota impacts the efficacy of immunotherapy in cancer patients – A recent literature survey – Stella Ziegler – European Journal of Microbiology & Immunology

Animal Microbiome

Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome – Tina Keller-Costa – Microbiome

Intestinal microbiome-mediated resistance against vibriosis for Cynoglossus semilaevis – Qian Zhou – Microbiome

Plant Microbiome

Response of soil microecology to different cropping practice under Bupleurum chinense cultivation – Li Liu – BMC Microbiology

Community Assembly of Fungi and Bacteria along Soil-Plant Continuum Differs in a Zoige Wetland – Jie Li – Microbiology Spectrum

Review: Investigating plant-microbe interactions within the root – Yuniar Devi Utami – Archives of Microbiology

Food Microbiome

Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation – Yuwei Tan – Microbiology Spectrum

More Microbes

A meta-analysis of acetogenic and methanogenic microbiomes in microbial electrosynthesis – Simon Mills – NPJ Biofilms and Microbiomes

Bioinformatics and Microbiome Analysis

MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes – Lin Zhang – PLoS Computational Biology

September 10, 2022

Human and General Microbiome

Evolution of the Gut Microbiome in HIV-Exposed Uninfected and Unexposed Infants during the First Year of Life – Conner L Jackson – mBio

Gastrointestinal microbiota profile and clinical correlations in advanced EGFR-WT and EGFR-mutant non-small cell lung cancer – Woraseth Saifon – BMC Cancer

Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome – Anuradha Ravi – Communications Biology

Genetic Determinants of Hydrogen Sulfide Biosynthesis in Fusobacterium nucleatum Are Required for Bacterial Fitness, Antibiotic Sensitivity, and Virulence – Yi-Wei Chen – mBio

Preprint: Genomic and ecologic characteristics of the airway microbial-mucosal complex – Leah Cuthbertson – BioXriv 

Beneficial Microbes and Compounds

Lactiplantibacillus plantarum Regulated Intestinal Microbial Community and Cytokines to Inhibit Salmonella typhimurium Infection – Rui-Han Liu – Probiotics and Antimicrobial Proteins

Animal Microbiome

Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach – Munni Khatoon – Gene

Plant Microbiome

The core bacterial microbiome of banana (Musa spp.) – Henry W G Birt – Environmental Microbiome

Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome – Yaping Guo – Environmental Microbiology

Environmental Microbiology

Virome analysis in lakes of the South Shetland Islands, Antarctica – 2020 – Tatiana Prado – The Science of the Total Environment

Bioinformatics and Microbiome Analysis

Investigating differential abundance methods in microbiome data: A benchmark study – Marco Cappellato – PLoS Computational Biology

A rapid and standardized workflow for functional assessment of bacterial biosensors in fecal samples – Ana Zúñiga – Frontiers in Bioengineering and Biotechnology

September 3, 2022

Highlights!!!

A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome – Shuqin Zeng – Nature Communications → Authors presented and described the main features of the  Early-Life Gut Genomes (ELGG) catalog: a dataset of 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3-years old from different regions.

A previously uncharacterized O-glycopeptidase from Akkermansia muciniphila requires the Tn-antigen for cleavage of the peptide bond – Brendon J Medley – The Journal of Biological Chemistry → AMUC_1438, a previously uncharacterized gene from A. muciniphila, encodes an O-glycopeptidase with mucin degrading capacity. This article shows relevant aspects of its enzymatic function. 

Lactic acid from vaginal microbiota enhances cervicovaginal epithelial barrier integrity by promoting tight junction protein expression – David Jose Delgado-Diaz – Microbiome → metaproteomic analysis on vaginal swab samples and transcriptomics analysis of cervicovaginal epithelial cell cultures showed that lactic acid, a commonly produced metabolite by the vaginal lactobacilli, is capable of enhancing genital epithelial barrier integrity; this microbial feature may help prevent invasion by sexually transmitted pathogens.

Human and General Microbiome

Review: A Perspective of the Urinary Microbiome in Lower Urinary Tract Infections – A Review – Rigoberto Pallares-Mendez – Current Urology Reports

Review: Methanogenic archaea in the human gastrointestinal tract – Christoph Hoegenauer – Nature Reviews. Gastroenterology & Hepatology

Meta-analysis of caries microbiome studies can improve upon disease prediction outcomes – Mark C Butcher – APMIS

Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure – Tatiana V Karpinets – BMC Cancer

Horizontal gene transfer enables programmable gene stability in synthetic microbiota – Teng Wang – Nature Chemical Biology

A Multiscale Spatiotemporal Model Including a Switch from Aerobic to Anaerobic Metabolism Reproduces Succession in the Early Infant Gut Microbiota – David M Versluis – mSystems

Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation – J Casper Swarte – Science Translational Medicine

Beneficial Microbes and Compounds

Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice – Weiling Guo – Probiotics and Antimicrobial Proteins

An Alternative Oat-Containing Ready-To-Use Therapeutic Food Does Not Alter Intestinal Permeability or the 16S rRNA Fecal Microbiome Configuration Among Children With Severe Malnutrition in Sierra Leone: A Randomized Controlled Trial – D Taylor Hendrixson – The Journal of Nutrition

Study on the Effect of Molecular Weight on the Gut Microbiota Fermentation Properties of Blackberry Polysaccharides In Vitro – Qiao-Yun Li – Journal of Agricultural and Food Chemistry

Animal Model Microbiome

Tissue-wide metabolomics reveals wide impact of gut microbiota on mice metabolite composition – Iman Zarei – Scientific Reports

Gut microbiota mediates the inhibition of lymphopoiesis in dietary-restricted mice by suppressing glycolysis – Si Tao – Gut Microbes

Non-Model Animal Microbiome

Limited microbiome differences in captive and semi-wild primate populations consuming similar diets – Sahana Kuthyar – FEMS Microbiology Ecology

Biodiversity, environmental drivers, and sustainability of the global deep-sea sponge microbiome – Kathrin Busch – Nature Communications

Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts – Yujie Meng – Microbiome

Mucin O-glycan-microbiota axis orchestrates gut homeostasis in a diarrheal pig model – Bing Xia – Microbiome

Plant Microbiome

Stressful, isolated, yet diverse: Green roofs have rich microbiomes that are not dominated by oligotrophic taxa – Antoine Hénault – Environmental Microbiology Reports

Nodulation and nitrogen fixation in Medicago truncatula strongly alters the abundance of its root microbiota and subtly affects its structure – Andrzej Tkacz – Environmental Microbiology

Bioinformatic Tools and Microbiome Analysis Techniques

Gut bacterial nutrient preferences quantified in vivo – Xianfeng Zeng – Cell

Metric learning for comparing genomic data with triplet network – Zhi Ma – Briefings in Bioinformatics

STENSL: Microbial Source Tracking with ENvironment SeLection – Ulzee An – mSystems

Review: Emerging microfluidic technologies for microbiome research – Yue Yu – Frontiers in Microbiology

August 16, 2022

Human and General Microbiome

Crohn’s disease in endoscopic remission, obesity, and cases of high genetic risk demonstrates overlapping shifts in the colonic mucosal-luminal interface microbiome – Jonathan P Jacobs – Genome Medicine

Preservation of fecal microbiome is associated with reduced severity of Graft-versus-Host Disease – Marina Burgos da Silva – Blood

Cobamide Sharing Is Predicted in the Human Skin Microbiome – Mary Hannah Swaney – mSystems

Postnatal exposure to ambient air pollutants is associated with the composition of the infant gut microbiota at 6-months of age – Maximilian J Bailey – Gut Microbes

Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites – Qingzhen Wei – Frontiers in Microbiology

Review: Recent insights into the role of microbiome in the pathogenesis of obesity – Eduard W J van der Vossen – Therapeutic Advances in Gastroenterology

Model Animal Microbiome

Impact of habitual chewing on gut motility via microbiota transition – Fukie Yaoita – Scientific Reports

Resources to Facilitate Use of the Altered Schaedler Flora (ASF) Mouse Model to Study Microbiome Function – Alexandra Proctor – mSystems

Non-model Animal Microbiome

The microbiome of a bacterivorous marine choanoflagellate contains a resource-demanding obligate bacterial associate – David M Needham – Nature Microbiology

Characterization of presence and activity of microRNAs in the rumen of cattle hints at possible host-microbiota cross-talk mechanism – Sara Ricci – Scientific Reports

Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts – Min Hui – PeerJ

Systematic profiling of the chicken gut microbiome reveals dietary supplementation with antibiotics alters expression of multiple microbial pathways with minimal impact on community structure – Angela Zou – Microbiome

Environmental Microbiome

Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction – Alessandro Rossi – Microbiome

Food Microbiome

Microbiome and Metabiotic Properties of Kefir Grains and Kefirs Based on Them –  Ding Fan – Microbiology

Profiling the role of microorganisms in quality improvement of the aged flue-cured tobacco – Xinying Wu – BMC Microbiology

August 6, 2022

Human and General Microbiome

The oral microbiome and lung cancer risk: An analysis of 3 prospective cohort studies – Emily Vogtmann – Journal of the National Cancer Institute

Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries – M J Carvalho – Nature Microbiology

Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer – Namjoo Kim – Scientific Reports

Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome – Zhiguo Zhang – Environmental Science & Technology

Review: Porphyromonas gingivalis and dental stem cells crosstalk amplify inflammation and bone loss in the periodontitis niche – Devaraj Ezhilarasan – Journal of Cellular Physiology

Beneficial Microbes and Compounds

On the effect of flavonoids and dietary fibre in lingonberries on atherosclerotic plaques, lipid profiles and gut microbiota composition in Apoe(-/-) mice – Jiyun Liu – International Journal of food Sciences and Nutrition

The Gut-Brain-Microbiome Connection: Can Probiotics Decrease Anxiety and Depression? – Jennifer Maybee – Issues in Mental Health Nursing

The effect of Lactobacillus rhamnosus B10 on alcoholic liver injury and intestinal microbiota in alcohol-induced mice model – Xia Li – Journal of Food Biochemistry

Model Animal Microbiome

The effect of young blood plasma administration on gut microbiota in middle-aged rats – Taha Ceylani – Archives of Microbiology

Non-Model Animal Microbiome

Quantitative microbial population study reveals geographical differences in bacterial symbionts of Ixodes ricinus – Aleksandra I Krawczyk – Microbiome

Host taxonomy determines the composition, structure, and diversity of the earthworm cast microbiome under homogenous feeding conditions – Manuel Aira – FEMS Microbiology Ecology

Ruminal Microbiota Determines the High-Fiber Utilization of Ruminants: Evidence from the Ruminal Microbiota Transplant – Xiaodong Chen – Microbiology Spectrum

Bioinformatics and Microbiome Analysis Techniques

Computational approach to modeling microbiome landscapes associated with chronic human disease progression – Lu Li – PLoS Computational Biology

Guideline for the analysis of the microbial communities of the human upper airways – Leonardo Mancabelli – Journal of Oral Microbiology