January 28, 2022

Human and General Microbiome

Diet leaves a genetic signature in a keystone member of the gut microbiota – Tanja Dapa – Cell Host & Microbe

Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis – Skye Rs Fishbein – eLife

Large-scale characterization of the macrolide resistome reveals high diversity and several new pathogen-associated genes – David Lund – Microbial Genomics

The small bowel microbiome changes significantly with age and aspects of the ageing process – Gabriela Leite – Microbial Cell

Intestinal microbiota profiles in a genetic model of colon tumorigenesis correlates with colon cancer biomarkers – Francesco Vitali – Scientific Reports

Skin microbiome profile of healthy Cameroonians and Japanese – Kazuhiro Ogai – Scientific Reports

Interactions between human milk oligosaccharides, microbiota and immune factors in milk of women with and without mastitis – Irma Castro – Scientific Reports

Microbiota of the prostate tumor environment investigated by whole-transcriptome profiling – Paul Vinu Salachan – Genome Medicine

Preview: Microbiome engineering: Taming the untractable – James W Marsh – Cell

Review: Microbiomes in physiology: Insights into 21(st) century global medical challenges – Emad Shehata – Experimental Physiology

Respiratory Tract Microbiome – Highlights

Gut microbiota dynamics in a prospective cohort of patients with post-acute COVID-19 syndrome – Qin Liu – Gut

Characteristics of Lung Microbiota in Children’s Refractory Mycoplasma pneumoniae Pneumonia Coinfected with Human Adenovirus B – Wenxiang Zhou – The Canadian Journal of Infectious Diseases & Medical Microbiology

The lung microbiota in children with cystic fibrosis captured by induced sputum sampling – Rebecca Weiser – Journal of Cystic Fibrosis 

Beneficial Microbes and Compounds

Bifidobacterium animalis subsp. lactis BB-12 Has Effect Against Obesity by Regulating Gut Microbiota in Two Phases in Human Microbiota-Associated Rats – Kemin Mao – Frontiers in Nutrition

Effects of a 10-Strain Oral Probiotic on Parameters of Vaginal Health and Microbial Community: A Pilot Clinical Study – Christopher J Martoni – International Journal of Women’s Health

A randomised, double-blind, placebo-controlled trial of Bifidobacterium bifidum CCFM16 for manipulation of the gut microbiota and relief from chronic constipation – Luyao Wang – Food & Function

Vaginal states: detection of conversion processes in women using contraception and characterization of vaginal Lactobacillus species – Sonia Elena María Fosch – Infectious Disorders Drug Targets

The probiotic properties and potential of vaginal Lactobacilli spp. isolated from healthy women against some vaginal pathogens – Arezoo Asadi – Letters in Applied Microbiology

Review: Protective Effects of Natural Polysaccharides on Intestinal Barrier Injury: A Review – Jiaying Huo – Journal of Agricultural and Food Chemistry

Animal Microbiome

Nitrogen recycling via gut symbionts increases in ground squirrels over the hibernation season – Matthew D Regan – Science

Robust host source tracking building on the divergent and non-stochastic assembly of gut microbiomes in wild and farmed large yellow croaker – Jun Zhu – Microbiome

Evaluation of three Bacillus spp. isolated from the gut of giant freshwater prawn as potential probiotics against pathogens causing Vibriosis and Aeromonosis – Muhamad Firdaus Syahmi Sam-On – Microbial Pathogenesis

Gut Microbial Trimethylamine is Elevated in Alcohol-Associated Hepatitis and Contributes to Ethanol-Induced Liver Injury in Mice – Robert N Helsley – eLife

Intestinal gluconeogenesis shapes gut microbiota, fecal and urine metabolome in mice with gastric bypass surgery – Justine Vily-Petit – Scientific Reports

Food Microbiome

To culture or not to culture: careful assessment of metabarcoding data is necessary when evaluating the microbiota of a modified-atmosphere-packaged vegetarian meat alternative throughout its shelf-life period – E Duthoo – BMC Microbiology

Plant Microbiome

Root Morphogenesis of Arabidopsis thaliana Tuned by Plant Growth-Promoting Streptomyces Isolated From Root-Associated Soil of Artemisia annua – Wenbo Fu – Frontiers in Plant Science

Environmental Microbiome

Soil microbial community development across a 32-year coastal wetland restoration time series and the relative importance of environmental factors – Katherine M Abbott – The Science of the Total Environment

Emerging frontiers in microbe mediated pesticide remediation: Unveiling role of omics and In silico approaches in engineered environment – Muneer Ahmad Malla – Environmental Pollution 

Review: Emerging investigator series: microplastic sources, fate, toxicity, detection, and interactions with micropollutants in aquatic ecosystems – a review of reviews – Mohamed Ateia – Environmental Science. Processes & Impacts

Techniques

Alternating Dual-Collision Energy Scanning Mass Spectrometry Approach: Discovery of Novel Microbial Bile-Acid Conjugates – Quan-Fei Zhu – Analytical Chemistry

Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus – Rebecca Lück – Applied Microbiology and Biotechnology

Lipidomics Analysis of Outer Membrane Vesicles and Elucidation of the Inositol Phosphoceramide Biosynthetic Pathway in Bacteroides thetaiotaomicron – Mariana G Sartorio – Microbiology Spectrum

January 26, 2022

General microbiome

[PREPRINT]Arresting microbiome development limits immune system maturation and resistance to infection – Lubin et al. – bioRxiv

Pregnancy and early life

Transcription shifts in gut bacteria shared between mothers and their infants – Vatanen et al. – Scientific Reports

Human urinary tract microbiome

Immune milieu and microbiome of the distal urethra in Ugandan men: impact of penile circumcision and implications for HIV susceptibility – Galwango et al. – Microbiome

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states – Adu-Oppong et al. – Microbiome

Longitudinal variability in the urinary microbiota of healthy premenopausal women and the relation to neighboring microbial communities: A pilot study – Biehl et al. – PLOS One

Human vaginal microbiome

molBV reveals immune landscape of bacterial vaginosis and predicts human papillomavirus infection natural history – Usyk et al. – Nature Communications

Human gut microbiome

Differences in gut microbiome by insulin sensitivity status in Black and White women of the National Growth and Health Study (NGHS): A pilot study – Price et al. – PLOS One

Changes in the gut microbiota and risk of colonization by multidrug-resistant bacteria, infection and death in critical care patients – Rubio et al. – Clinical Microbiology and Infection

[PREPRINT]Gut Microbiome of Helminth Infected Indigenous Malaysians Is Context Dependent – Tee et al. – bioRxiv

Assessing the joint effects of brain aging and gut microbiota on the risks of psychiatric disorders – Zhang et al. – Brain Imaging and Behavior

Animal microbiome

Investigation of fiber utilization in the rumen of dairy cows based on metagenome-assembled genomes and single-cell RNA sequencing – Xue et al. – Microbiome

The influence of food processing methods on serum parameters, apparent total-tract macronutrient digestibility, fecal microbiota and SCFA content in adult beagles – Cai et al. – PLOS One

Kaempferol acts on bile acid signaling and gut microbiota to attenuate the tumor burden in ApcMin/+ mice – Li et al. – European Journal of Pharmacology

[PREPRINT]Diet outweighs genetics in shaping gut microbiomes in Asian honeybee – Su et al. – bioRxiv

Changes of Gut Microbiota by Natural mtDNA Variant Differences Augment Susceptibility to Metabolic Disease and Ageing – Künstner et al. – Int. J. Mol. Sci.

Diet Prevents Social Stress-Induced Maladaptive Neurobehavioural and Gut Microbiota Changes in a Histamine-Dependent Manner – Costa et al. – Int. J. Mol. Sci.

Gut microbe-targeted choline trimethylamine lyase inhibition improves obesity via rewiring of host circadian rhythms – Schugar et al. – eLife

Limited Evidence for Microbial Transmission in the Phylosymbiosis between Hawaiian Spiders and Their Microbiota – Perez-Lamarque – mSystems

Parkinson’s Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats – van Kessel et al. – mSystems

Multi-omics Analysis Revealed Coordinated Responses of Rumen Microbiome and Epithelium to High-Grain-Induced Subacute Rumen Acidosis in Lactating Dairy Cows – Mu et al. – mSystems

Predicting fungal infection rate and severity with skin-associated microbial communities on amphibians – Chen et al. – Molecular Ecology

Commensal oral microbiota induces osteoimmunomodulatory effects separate from systemic microbiome in mice – Hathaway-Schrader et al. – JCI insight

Plant, root, and soil microbiome

Shared features and reciprocal complementation of the Chlamydomonas and Arabidopsis microbiota – Duran et al. – Nature Communications

[PREPRINT]Biodiversity of the Genus Trichoderma in the Rhizosphere of Coffee (Coffea arabica) Plants in Ethiopia and their Potential Use in Biocontrol of Coffee Wilt Disease – Mulatu et al. – bioRxiv

Built environment (subways, indoor surfaces)

A biogeographic 16S rRNA survey of bacterial communities of ureolytic biomineralization from California public restrooms – Lim et al. – PLOS One

Techniques

[PREPRINT]Choice of 16S ribosomal RNA primers impacts urinary microbiota profiling – Heidrich et al. – bioRxiv

January 21, 2022

Human and General Microbiome

Metabolite-based dietary supplementation in human type 1 diabetes is associated with microbiota and immune modulation – Kirstine J Bell – Microbiome

GWAS-associated bacteria and their metabolites appear to be causally related to the development of inflammatory bowel disease – Zhenhuang Zhuang – European Journal of Clinical Nutrition

The vaginal Torquetenovirus titer varies with vaginal microbiota composition in pregnant women – Tania Regina Tozetto-Mendoza – PloS ONE

Can the Acid-formation Potential of Saliva Detect a Caries-related Shift in the Oral Microbiome? – Cornelia Frese – Oral Health & Preventive Dentistry

Gut microbiome alterations and gut barrier dysfunction are associated with host immune homeostasis in COVID-19 patients – Zhonghan Sun – BMC Medicine

Predicting Treatment Nonresponse in Hispanic/Latino Children Receiving Silver Diamine Fluoride for Caries Arrest: A Pilot Study Using Machine Learning – Ryan Richard Ruff – Frontiers in Oral Health

The Gut Microbiome of Adults With Type 1 Diabetes and Its Association With the Host Glycemic Control – Smadar Shilo – Diabetes Care

Evaluation of Bacterial Diversity and Evolutionary Dynamics of Gut Bifidobacterium longum Isolates Obtained from Older Individuals in Hubei Province, China – Zhendong Zhang – Microbiology Spectrum

Review: Frontiers in Oral Mucosal Immunity and the Microbiome – Georgios N Belibasakis – Frontiers in Oral Health

Review: The microbiota-gut-brain axis: pathways to better brain health. Perspectives on what we know, what we need to investigate and how to put knowledge into practice – Anirikh Chakrabarti – Cellular and Molecular Life Sciences

Meta-Analysis: Predictors of Fecal Microbiota Transplant Failure in Clostridioides difficile Infection: An Updated Meta-analysis – Azizullah Beran – Journal of Clinical Gastroenterology

Systematic Review: The Role of Gut Microbiota-Brain Axis in Pathophysiology of ADHD: A Systematic Review – Salman Shirvani-Rad – Journal of Attention Disorders

Systematic Review: Meta-Analysis Using NGS Data: The Veillonella Species in Dental Caries – Naile Dame-Teixeira – Frontiers in Oral Health

Beneficial Microbes and Compounds

Peppermint oil effects on the gut microbiome in children with functional abdominal pain – Santosh Thapa – Clinical and Translational Science

SER-109, an Oral Microbiome Therapy for Recurrent Clostridioides difficile Infection – Paul Feuerstadt – The New England Journal of Medicine

Lactiplantibacillus plantarum CCFM1019 attenuate polycystic ovary syndrome through butyrate dependent gut-brain mechanism – Yufeng He – Food & Function

Causal relationship between gut microbiota and serum vitamin D: evidence from genetic correlation and Mendelian randomization study – Xiaolin Yang – European Journal of Clinical Nutrition

Review: Modulation of Gut Microbiota and Immune System by Probiotics, Pre-biotics, and Post-biotics – Yue Liu – Frontiers in Nutrition

Review: Outlook on next-generation probiotics from the human gut – Francesca De Filippis – Cellular and Molecular Life Sciences

Animal Microbiome

Seasonal shift of the gut microbiome synchronizes host peripheral circadian rhythm for physiological adaptation to a low-fat diet in the giant panda – Guangping Huang – Cell Reports

Seasonal variations in the composition and functional profiles of gut microbiota reflect dietary changes in plateau pikas – Chao Fan – Integrative Zoology

N-acyl-homoserine lactone produced by Rahnella inusitata isolated from the gut of Galleria mellonella influences Salmonella phenotypes – Leonardo Luiz de Freitas – Brazilian Journal of Microbiology

Comparative 16S Metabarcoding of Nile Tilapia Gut Microbiota from the Northern Lakes of Egypt – Ahmed M Serag – Applied Biochemistry and Biotechnology

Diversity and Distribution of Microbial Communities Associated with Reef Corals of the Malay Peninsula – Dhivya P Kanisan – Microbial Ecology

The Harris’ hawk (Parabuteo unicinctus) as a source of pathogenic human yeasts: a potential risk to human health – Gustavo Dornelles – Future Microbiology

Increased microbial diversity and decreased prevalence of common pathogens in the gut microbiomes of wild turkeys compared to domestic turkeys – Julia Craft – Applied and Environmental Microbiology

Comparative Evaluation of the Effect of Metformin and Insulin on Gut Microbiota and Metabolome Profiles of Type 2 Diabetic Rats Induced by the Combination of Streptozotocin and High-Fat Diet – Nan Hu – Frontiers in Pharmacology

Plant Microbiome

Modulating the rhizosphere microbiome by altering the cocktail of root secretions – Wei Zhang – Plant Physiology

Book Chapter: Characterization of Tobacco Microbiome by Metagenomics Approach – R Suresh Kumar – Methods in Molecular Biology 

Bioinformatics and Genomics

Incorporating genome-based phylogeny and functional similarity into diversity assessments helps to resolve a global collection of human gut metagenomes – Nicholas D Youngblut – Environmental Microbiology

Single-cell Microbiomics Unveils Distribution and Patterns of Microbial Symbioses in the Natural Environment – Vittorio Boscaro – Microbial Ecology

Adaptive and powerful microbiome multivariate association analysis via feature selection – Kalins Banerjee – NAR Genomics and Bioinformatics

Metabolic modeling of host-microbe interactions for therapeutics in colorectal cancer – Prerna Bhalla – NPJ Systems Biology and Applications

January 18, 2022

Today’s digest contains interesting gut-brain axis articles, developments in bioinformatic multi-omic analyses, and some recent developments in long COVID research highlighted under non microbiome picks below. 

General microbiome

Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states – Adu oppong et al. – Microbiome 

Human gut microbiome

Gut Ruminococcaceae levels at baseline correlate with risk of antibiotic-associated diarrhea – Gu et al. – iScience

Home or hospital birth: the neonatal microbiota perspective – Stojanov et al. – The Lancet Microbe

A pilot exploration of multi-omics research of gut microbiome in major depressive disorders – Zhao et al – Translational Psychiatry

Post-ischemic protein restriction induces sustained neuroprotection, neurological recovery, brain remodeling, and gut microbiota rebalancing – de Carvalho et al. – Brain Behavior and Immunity

Bifidobacterium breve CCFM1025 attenuates major depression disorder via regulating gut microbiome and tryptophan metabolism: A randomized clinical trial – Tian et al.  – Brain Behavior and Immunity

Gestational insulin resistance is mediated by the gut microbiome-indoleamine 2,3-dioxygenase axis – Priyadarshini et al. – Gastroenterology

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

Virome

[Research Highlight] Virome holds back a vaccine – York – Nature Reviews Microbiology

Plant & Soil microbiome

Genome-Resolved Metagenomics Reveals Distinct Phosphorus Acquisition Strategies between Soil Microbiomes – Wu et al. – mSystems

Bioinformatics

M&Ms: a versatile software for building microbial mock communities – García-García et al. – Bioinformatics

GraphOmics: an interactive platform to explore and integrate multi-omics data – Wandy & Daly – BMC Bioinformatics

Aristotle: stratified causal discovery for omics data – Mansouri et al.  – BMC Bioinformatics

Non Microbiome Picks

The last few weeks has seen several big studies of ‘long COVID’ published, as well as a letter in The Guardian, which I wanted to highlight

Immunological dysfunction persists for 8 months following initial mild-to-moderate SARS-CoV-2 infection – Phetsouphanh et al. – Nature Immunology

Long-term perturbation of the peripheral immune system months after SARS-CoV-2 infection – Ryan et al. BMC Medicine

Post-acute neurological consequences of COVID-19: an unequal burden – Nolen et al. – Nature Medicine 

Long COVID in children – Gurdasani et al. – The Lancet Child Adolescent Health
I’m leading a long Covid trial – it’s clear Britain has underestimated its impact – Amitava Banerjee – The Guardian

January 12, 2022

General microbiome

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

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

Human endometrial microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

Bioinformatics

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

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

Techniques

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

January 10, 2022

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


Gut microbiome

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

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

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

Urinary microbiome

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

Vaginal microbiome

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

Skin microbiome

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

Water microbiome

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

Animal microbiome

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

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

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

Techniques and methods

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

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

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

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

Bioinformatics

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

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



January 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 22, 2021

General microbiome

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

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

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

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

Pregnancy and early life

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

Human oral microbiome

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

Human skin microbiome

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

Human vaginal microbiome

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

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

Human gut microbiome

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

Techniques

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

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

December 20, 2021

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

General microbiome

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

Human vaginal microbiome

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

Human gut microbiome

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

Animal microbiome

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

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

Plant, root, and soil microbiome

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

Built environment

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

Phages and viruses

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

Bioinformatics

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

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

Kara’s non-microbiology pick

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

November 10, 2021

Human urinary tract microbiome

[PREPRINT]Recurrent urinary tract infection and estrogen shape the taxonomic ecology and functional potential of the postmenopausal urobiome – Neugent et al. – bioRxiv

Human gut microbiome

The Impact of a Mediterranean Diet on the Gut Microbiome in Healthy Human Subjects: A Pilot Study – Rejeski et al. – Digestion

Altered diversity and composition of gut microbiota in patients with allergic rhinitis – Zhou et al. – Microbial Pathogenesis

Fecal Microbiome Transplantation for Recurrent Clostridioides difficile Infection: Treatment Efficacy, Short and Long-term Follow-up Results from Consecutive Case Series – Urbonas et al. – Journal of Gastrointestinal and Liver Diseases

Donor screening for fecal microbiota transplantation in China: Evaluation of 8,483 candidates – Zhang et al. – Gastroenterology

Faecal microbial biomarkers in early diagnosis of colorectal cancer – Olovo et al. – Journal of Cellular and Molecular Medicine

Hepatocellular Cancer and Gut Microbiome: Time to Untie Gordian’s Knot – Aygün & Tözün – Journal of Gastrointestinal Cancer

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

Cinnamic acid suppresses bone loss via induction of osteoblast differentiation with alteration of gut microbiota – Hong et al. – The Journal of Nutritional Biochemistry

Gut microbiome affects the metabolism of metronidazole in mice through regulation of hepatic cytochromes P450 expression – Zemanová et al. – PLOS One

Animal microbiome (for animals in the wild)

[PREPRINT]Maternal effects on early-life gut microbiome maturation in a wild nonhuman primate – Baniel et al. – bioRxiv

Evidence of MHC class I and II influencing viral and helminth infection via the microbiome in a non-human primate – Montero et al. – PLOS Pathogens

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

Plant, root, and soil microbiome

Artificial selection of stable rhizosphere microbiota leads to heritable plant phenotype changes – Jacquiod et al. – Ecology Letters

Plastic mulch debris in rhizosphere: Interactions with soil-microbe-plant systems – Liu et al. – Science of The Total Environment

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

[PREPRINT]Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens – Numberger et al. – bioRxiv

Bioinformatics

[PREPRINT]specificity : an R package for generalized specificity analysis, with example analyses of Hawaiian foliar endophytic Fungi, human gut microbiome bacteria, and Antarctic glacier bacteria – Darcy et al. – bioRxiv

[PREPRINT]Unifying the known and unknown microbial coding sequence space – Vanni et al. – bioRxiv

Identifying prognostic pairwise relationships among bacterial species in microbiome studies – Devlin, Martin & Ostrovnaya – PLOS Computational Biology

HashSeq: a Simple, Scalable, and Conservative De Novo Variant Caller for 16S rRNA Gene Data Sets – Fouladi, Young & Fodor – mSystems