Category Archives: Human oral

April 20, 2022

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General microbiome

How the gut talks to the brain – Adamantidis – Science

Pregnancy and early life

Relationship between gut microbiome characteristics and the effect of nutritional therapy on glycemic control in pregnant women with gestational diabetes mellitus – Chen et al. – PLOS One

Dynamics of the infant gut microbiota in the first 18 months of life: the impact of maternal HIV infection and breastfeeding – Grant-Beurmann et al. – Microbiome

Human respiratory microbiome

The diagnostic value of nasal microbiota and clinical parameters in a multi-parametric prediction model to differentiate bacterial versus viral infections in lower respiratory tract infections – Li et al. – PLOS One

Human skin microbiome

The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes – Verbanic, Deacon & Chen – Microbiology Spectrum

Human vaginal microbiome

Vaginal microbiota as an unusual cause of spondylodiscitis – Kolakowska et al. – Archives of Gynecology and Obstetrics

Human gut microbiome

Environmental factors shaping the gut microbiome in a Dutch population – Gacesa et al. – Nature

Predictive Role of Gut Microbiota in Weight Loss Achievement after Bariatric Surgery – Gutierrez-Repiso et al. – Journal of the American College of Surgeons

Intestinal Blautia may protect against neutropenic fever in allogeneic transplant patients by augmenting the intestinal epithelium – Rashidi et al. – Clinical Infectious Diseases

Clinical Observation of the Effects of Oral Opioid on Inflammatory Cytokines and Gut Microbiota in Patients with Moderate to Severe Cancer Pain: A Retrospective Cohort Study – Wang et al. – Pain and Therapy

The human gut microbiota contributes to type-2 diabetes non-resolution 5-years after Roux-en-Y gastric bypass – Debedat et al. – Gut Microbes

The gut microbial metabolite formate exacerbates colorectal cancer progression – Ternes et al. – Nature Metabolism

Drinking water chlorination has minor effects on the intestinal flora and resistomes of Bangladeshi children – Nadimpalli et al. – Nature Microbiology

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

The microbiota-gut-brain axis participates in chronic cerebral hypoperfusion by disrupting the metabolism of short-chain fatty acids – Xiao et al. – Microbiome

Effect of gluten-free diet and antibiotics on murine gut microbiota and immune response to tetanus vaccination – Kihl et al. – PLOS One

Hawk tea prevents high-fat diet-induced obesity in mice by activating the AMPK/ACC/SREBP1c signaling pathways and regulating the gut microbiota – Tao et al. – Food & Function

Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy – Guo et al. – Journal of Applied Microbiology

The gut microbiome influences host diet selection behavior – Trevelline & Kohl – PNAS

High-fat diet disrupts REG3γ and gut microbial rhythms promoting metabolic dysfunction – Frazier et al. – Cell Host & Microbe

Animal microbiome (for animals in the wild)

Intrinsic and extrinsic factors influence on an omnivore’s gut microbiome – Trujillo et al. – PLOS One

Effects of Schyzocotyle acheilognathi (Yamaguti, 1934) infection on the intestinal microbiota, growth and immune reactions of grass carp (Ctenopharyngodon idella) – Fu et al. – PLOS One

Virome in the cloaca of wild and breeding birds revealed a diversity of significant viruses – Shan et al. – Microbiome

Interspecies microbiome transplantation recapitulates microbial acquisition in mosquitoes – Coon, Hedge & Hughes

Gut microbiota promote biotransformation and bioaccumulation of arsenic in tilapia – Environmental Pollution

Plant, root, and soil microbiome

Linnemannia elongata (Mortierellaceae) stimulates Arabidopsis thaliana aerial growth and responses to auxin, ethylene, and reactive oxygen species – Vandepol et al. – PLOS One

Bacterial and fungal microbiota of total mixed ration silage stored at various temperatures – Wali et al. – Journal of Applied Microbiology

Bioinformatics

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community – Lyalina – PLOS One

Techniques

THOR’s Hammer: the Antibiotic Koreenceine Drives Gene Expression in a Model Microbial Community – Hurley et al. – mBio

Microbes in the news

Bacteria generate electricity from methane

April 6, 2022

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Today’s digest features studies on microbial genes of unknown function, oral microbiome of smokeless tobacco consumers, non-industrialized infant microbiome, and more news. Happy reading!

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Global microbiome

Global Distribution of mcr Gene Variants in 214K Metagenomic Samples – Hannah-Marie Martiny – mSystems

Symposium Review: After the storm—Perspectives on the taxonomy of Lactobacillaceae – Nanzhen Qiao – JDS Communications

Oral microbiome

Assessing the Effect of Smokeless Tobacco Consumption on Oral Microbiome in Healthy and Oral Cancer Patients – Rituja Saxena – Frontiers in Cellular and Infection Microbiology

Gut microbiome

Unravelling specific diet and gut microbial contributions to inflammatory bowel disease – Gabriel Vasconcelos Pereira – bioRxiv

Effects of caloric restriction on the gut microbiome are linked with immune senescence – Julia Sbierski-Kind – Microbiome

Tap water as a natural vehicle for microorganisms shaping the human gut microbiome – Gabriele Andrea Lugli – Environmental Microbiology

Review: Diet-gut microbiota interactions on cardiovascular disease – Xufei Zhang and Philippe Gérard – Computational and Structural Biotechnology Journal

*Robust Variation in Infant Gut Microbiome Assembly Across a Spectrum of Lifestyles – Matthew R Olm – bioRxiv

Animal microbiome

Extensive metagenomic analysis of the porcine gut resistome to identify indicators reflecting antimicrobial resistance – Yunyan Zhou – Microbiome

Animal experiment

Modulation of the gut microbiome by novel synthetic glycans for the production of propionate and the reduction of cardiometabolic risk factors – Yves A Millet – bioRxiv

Plant microbiome

The phyllosphere microbiome shifts toward combating melanose pathogen – Pu-Dong Li – Microbiome

Wastewater microbiome

Near-neutral pH increased n-caprylate production in a microbiome with product inhibition of methanogenesis – Rodolfo Palomo-Briones – bioRxiv

Techniques

Review: Next-generation sequencing: insights to advance clinical investigations of the microbiome – Caroline R. Wensel – The Journal of Clinical Investigations

Metagenomics-enabled microbial surveillance – Karrie K. K. Ko – Nature Microbiology

Bioinformatics

Software testing in microbial bioinformatics: a call to action – Boas C.L. van der Putten – Microbial Genomics

Review: Machine Learning and Deep Learning Applications in Metagenomic Taxonomy and Functional Annotation – Alban Mathieu – Frontiers in Microbiology

*Unifying the known and unknown microbial coding sequence space – Chiara Vanni – eLife

NSURP is a community-driven initiative to create rewarding remote summer research opportunities for BIPOC and Latinx undergraduate students in the Microbiology, Immunology, and Cancer Biology Sciences.

March 31, 2022

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General microbiome

Whole genome sequencing and gene sharing network analysis powered by machine learning identifies antibiotic resistance sharing between animals, humans and environment in livestock farming – Peng et al. – PLOS Computational Biology

[PREPRINT]Superfast Evolution of Multi-drug Antibiotic Resistance – Zhang et al. – bioRxiv

Pregnancy and early life

Identification of the specific microbial community compositions in saliva associated with periodontitis during pregnancy – Narita & Kodama – Clinical Oral Investigations

Vaginal microbiome

Impact of Topical Interventions on the Vaginal Microbiota and Metabolome in Postmenopausal Women – Srinivasan et al. – JAMA Network Open

Human gut microbiome

[REVIEW]The interplay between anticancer challenges and the microbial communities from the gut – Hobson et al. – European Journal of Clinical Microbiology & Infectious Diseases

[EDITORIAL]Unraveling disease pathways involving the gut microbiota: the need for deep phenotyping and longitudinal data – Meyer et al. – The American Journal of Clinical Nutrition

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

The Effects of Stevia Consumption on Gut Bacteria: Friend or Foe? – Kasti et al. – Microorganisms

Jejunoileal mucosal growth in mice with a limited microbiome – Shaughnessy – PLOS One

Plant, root, and soil microbiome

Reproducible Propagation of Species-Rich Soil Bacterial Communities Suggests Robust Underlying Deterministic Principles of Community Formation – Causevic et al. – mSystems

Built environment (subways, indoor surfaces)

A quantitative microbial risk assessment for touchscreen user interfaces using an asymmetric transfer gradient transmission mode – di Battista – PLOS One

Forensics

Postmortem Skeletal Microbial Community Composition and Function in Buried Human Remains – Emmons et al. – mSystems

Bioinformatics

Microbial Identification Using rRNA Operon Region: Database and Tool for Metataxonomics with Long-Read Sequence – Seol et al. – Microbiology Spectrum

Techniques

Long-Term Incubation of Lake Water Enables Genomic Sampling of Consortia Involving Planctomycetes and Candidate Phyla Radiation Bacteria – Jaffe et al. – mSystems

March 30, 2022

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General microbiome

[REVIEW]Glycan processing in gut microbiomes – La Rosa et al. – Current Opinion in Microbiology

Multi-site human microbiome

[REVIEW]The Oral-Microbiome-Brain Axis and Neuropsychiatric Disorders: An Anthropological Perspective – Bowland & Weyrich – Frontiers in Psychiatry

Human oral microbiome

Microbial and molecular differences according to the location of head and neck cancers – Kim et al. – Cancer Cell International

Microbial differences between active and remission peri-implantitis – Hashimoto et al. – Scientific Reports

Human gut microbiome

Dynamics of the normal gut microbiota: A longitudinal one-year population study in Sweden – Olsson et al. – Cell Host & Microbe

Microbiota-microglia connections in age-related cognition decline – Zhou et al. – Aging Cell

Patients with psoriasis have a dysbiotic taxonomic and functional gut microbiota – Todberg – British Journal of Dermatology

[PREPRINT]Distinct Colon Mucosa Microbiomes associated with Tubular Adenomas and Serrated Polyps – Avelar-Barragan et al. – bioRxiv

Early prediction of incident liver disease using conventional risk factors and gut-microbiome-augmented gradient boosting – Liu et al. – Cell Metabolism

Insights from shotgun metagenomics into bacterial species and metabolic pathways associated with NAFLD in obese youth – Testerman et al. – Hepatology Commonications

Dietary Patterns and Gut Microbiota: the Crucial Actors in Inflammatory Bowel Disease – He et al. – Advances in Nutrition

A Guide to Dietary Pattern–Microbiome Data Integration – Choi et al. – The Journal of Nutrition

Functional Significance of Different Milk Constituents in Modulating the Gut Microbiome and Infant Health – Yadav et al. – J. Agric. Food Chem.

The gut microbiome as mediator between diet and its impact on immune function – Shi et al. – Scientific Reports

Differences in the intestinal microbiome associated with diarrhea during lenvatinib treatment for hepatocellular carcinoma – Inuai et al. – Digestive Diseases

16S rDNA sequencing analyzes differences in intestinal flora of human immunodeficiency virus (HIV) patients and association with immune activation – Mingjun et al. – Bioengineered

[REVIEW]Profile of Gut Microbiota of Adults with Diabetes Mellitus Type 1: A Systematic Review – Moreira et al. – Current Diabetes Reviews

Association between systemic lupus erythematosus and disruption of gut microbiota: a meta-analysis – Xiang et al. – Immunology and Inflammation

[REVIEW]The Bridge Between Ischemic Stroke and Gut Microbes: Short-Chain Fatty Acids – Fang et al. – Cellular and Molecular Neurobiology

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

Prophylactic effects of hyperforin on anhedonia-like phenotype in chronic restrain stress model: A role of gut microbiota – Zhang et al. – Letters in Applied Microbiology

Metabolome and microbiome multi-omics integration from a murine lung inflammation model of bronchopulmonary dysplasia – Saie et al. – Pediatric Research

Microbiome applications for laying hen performance and egg production – Ricke, Dittoe & Olson – Poultry Science

Animal microbiome (for animals in the wild)

[PREPRINT]The connection between the gut mycobiome community of natural black soldier fly populations and their environment – Vitenberg, Goldway & Opatovsky – bioRxiv

Inhibitory Bacterial Diversity and Mucosome Function Differentiate Susceptibility of Appalachian Salamanders to Chytrid Fungal Infection – Jimenez et al. – Applied and Environmental Microbiology

Composition and short-term stability of gut microbiota in lean and spontaneously overweight healthy Labrador retriever dogs – Söder et al. – Acta Veterinaria Scandinavica

Alterations in common marmoset gut microbiome associated with duodenal strictures – Sheh et al. – Scientific Reports

Plant, root, and soil microbiome

Spatial organization of the kelp microbiome at micron scales – Ramirez-Puebla et al. – Microbiome

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

Metagenomics reveals global-scale contrasts in nitrogen cycling and cyanobacterial light-harvesting mechanisms in glacier cryoconite – Marakami et al. – Microbiome

Bacterial communities in surface and basal ice of a glacier terminus in the headwaters of Yangtze River on the Qinghai–Tibet Plateau – Ren et al. – Envionmental Microbiome

Built environment (subways, indoor surfaces)

Multikingdom interactions govern the microbiome in subterranean cultural heritage sites – Liu et al. – PNAS

Indoor green can modify the indoor dust microbial communities – Dockx et al. – Indoor Air

Forensics

Microbial community succession of submerged bones in an aquatic habitat – Kaszubinski et al . – Journal of Forensic Sciences

Bioinformatics

Metagenomic strain detection with SameStr: identification of a persisting core gut microbiota transferable by fecal transplantation – Podlesny et al. – Microbiome

[PREPRINT]Detection of Parasites in Microbiomes using Metagenomics – Kirstagler, Aarestrup & Pamp – bioRxiv

Techniques

Tryptophan Supplementation Increases the Production of Microbial-Derived AhR Agonists in an In Vitro Simulator of Intestinal Microbial Ecosystem – Koper et al. – J. Agric. Food Chem.

March 02, 2022

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General microbiome

Bacterial-Fungal Interactions and Their Impact on Microbial Pathogenesis – MacAlpine, Robbins & Cowen – Molecular Ecology

Pregnancy and early life

Influence of timing of maternal antibiotic administration during caesarean section on infant microbial colonisation: a randomised controlled trial – Dierikx et al. – Gut

Human skin microbiome

Predominance of Staphylococcus correlates with wound burden and disease activity in dystrophic epidermolysis bullosa: a prospective case-control study – Reimer-Taschenbrecker et al. – Journal of Investigative Dermatology

[REVIEW]Towards standardized and reproducible research in skin microbiomes – Ruuskanen et al. – Environmental Microbiology

Human oral microbiome

Comparability of microbiota of swabbed and spit saliva – Kaan et al. – Oral Sciences

Human gut microbiome

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Shen et al. – Applied Microbial and Cell Physiology

Associations between Drinking Water Source and Gut Microbiota Composition in the American Gut Project Database – Vanhaecke – Annals of Nutrition and Metabolism

Rethinking Parkinson Disease: Exploring Gut-Brain Interactions and the Potential Role of Exercise – Zapanta et al. – Physical Therapy & Rehabilitation Journal

[PREPRINT]Mucosal microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients – Tran et al. – bioRxiv

How to Maintain a Healthy Gut Microbiome in Children with Cancer? Gut Microbiome Association with Diet in Children with Solid Tumors Postchemotherapy – Zhou et al. – OMICS: A Journal of Integrative Biology

[REVIEW]The potential utility of fecal (or intestinal) microbiota transplantation in controlling infectious diseases – Ghani et al. – Gut Microbes

Cross-cohort gut microbiome associations with immune checkpoint inhibitor response in advanced melanoma – Lee et al. – Nature Medicine

Intestinal microbiota signatures of clinical response and immune-related adverse events in melanoma patients treated with anti-PD-1 – McCulloch et al. – Nature Medicine

Establishing the role of the gut microbiota in susceptibility to recurrent urinary tract infections – Worby et al. – JCI

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

High environmental temperature: Insights into behavioural, neurodevelopmental and gut microbiome changes following gestational exposure in rats – Adebiyi – Neuroscience

Animal microbiome (for animals in the wild)

Unraveling the microbiota of the fish parasite Pseudoterranova decipiens in codfish (Gadus morhua) reveals a fish-related bacterial community – Saelens & Houf – International Journal of Food Microbiology

Microbial biogeography of the wombat gastrointestinal tract – Eisenhofer et al. – PeerJ

Intrinsic variation in the vertically transmitted core virome of the mosquito Aedes aegypti – Coatsworth et al. – Molecular Ecology

Plant, root, and soil microbiome

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain – Pang et al. – Microbiology Spectrum

Long-term effect of epigenetic modification in plant–microbe interactions: modification of DNA methylation induced by plant growth-promoting bacteria mediates promotion process – Chen et al. – Microbiome

Bioinformatics

[PREPRINT]Achieving pan-microbiome biological insights via the dbBact knowledge base – Amir et al. – bioRxiv

January 19, 2022

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Human oral and skin microbiome

Oral HPV associated with differences in oral microbiota beta diversity and microbiota abundance – Zhang et al. – The Journal of Infectious Diseases

The Skin and Nose Microbiome and Its Association with Filaggrin Gene Mutations in Pediatric Atopic Dermatitis – van Mierlo et al. – Dermatology

Human gut microbiome

Associations of Childhood and Perinatal Blood Metals with Children’s Gut Microbiomes in a Canadian Gestation Cohort – Shen et al. – Environmental Health Perspectives

Patient knowledge of gut microbiota and acceptability of fecal microbiota transplantation in various diseases – Benech et al. – Neurogastroenterology & Motility

[PREPRINT]Comprehensive assessment of functional effects of commonly used sweeteners on ex vivo human gut microbiome – Sun et al. – bioRxiv

Fusobacterium nucleatum and Bacteroides fragilis detection in colorectal tumours: Optimal target site and correlation with total bacterial load – Rye et al. – PLOS One

Human gut microbiome aging clocks based on taxonomic and functional signatures through multi-view learning – Chen et al. – Gut Microbes

[REVIEW]The gut microbiome can be a potential regulator and treatment target of bone metastasis – Contino, Yadav & Shiozawa – Biochemical Pharmacology

Animal microbiome

Comparative analysis of gut microbial composition and potential functions in captive forest and alpine musk deer – Jiang et al. – Environmental Biotechnology

Effects of dietary antimicrobial peptides on intestinal morphology, antioxidant status, immune responses, microbiota and pathogen disease resistance in grass carp Ctenopharyngodon idellus – Liu et al. – Microbial Pathogenesis

[PREPRINT]Microbiomes of hadal fishes contain similar taxa, obligate symbionts, and known piezophiles across trench habitats – Blanton et al. – bioRxiv

Association of human disturbance and gastrointestinal parasite infection of yellow baboons in western Tanzania – Mason et al. – PLOS One

Bacterial recognition by PGRP-SA and downstream signalling by Toll/DIF sustain commensal gut bacteria in Drosophila – Bahuguna et al. – PLOS Genetics

[PREPRINT]Meta-analysis of the black soldier fly (Hermetia illucens) microbiota based on 16S rRNA gene amplicon sequencing – Idema et al. – bioRxiv

Groundwater microbiome

Vertical stratification of microbial communities and isotope geochemistry tie groundwater denitrification to sampling location within a nitrate-contaminated aquifer – Chakraborty et al. – Science of The Total Environment

Techniques / Bioinformatics

Microbiome differential abundance methods produce different results across 38 datasets – Nearing et al. – Nature Communications

[PREPRINT]Using strain-resolved analysis to identify contamination in metagenomics data – Lou et al. – bioRxiv

Revealing General Patterns of Microbiomes That Transcend Systems: Potential and Challenges of Deep Transfer Learning – David et al. – mSystems

January 12, 2022

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General microbiome

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

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

Human endometrial microbiome

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

Human oral microbiome

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

Human gut microbiome

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

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

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

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

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

Animal microbiome

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

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

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

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

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

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

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

Plant, root, and soil microbiome

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

Bioinformatics

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

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

Techniques

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

December 22, 2021

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General microbiome

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

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

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

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

Pregnancy and early life

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

Human oral microbiome

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

Human skin microbiome

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

Human vaginal microbiome

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

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

Human gut microbiome

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

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

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

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

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

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

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

Animal microbiome (for animals in the wild)

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

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

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

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

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

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

Plant, root, and soil microbiome

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

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

Techniques

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

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

December 15, 2021

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Nasal microbiome

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

Pregnancy and early life

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

Multi-site human microbiome

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

Human oral microbiome

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

Human eye microbiome

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

Human vaginal microbiome

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

Human gut mycobiome/microbiome

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

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

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

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

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

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

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

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

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

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

Bioinformatics / Databases

Cow Rumen v1.0 – Database

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

Microbiome podcast

The Microbiome Facts, Not the Hype – Kristina Campbell

December 14, 2021

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Today’s digest contains several great recent papers, but in particular I’d like to highlight a Nature Methods paper on applying network biology approaches to the microbiome, and a Nature paper which disentangles the effects of drugs and disease on host and microbiome.

General microbiome

Fast and flexible analysis of linked microbiome data with mako – Röttjers & Faust – Nature Methods. 

Combinatorial, additive and dose-dependent drug–microbiome associations – Forslund et al. Nature 

Mammalian gut metabolomes mirror microbiome composition and host phylogeny – Gregor et al. – ISME 

Human gut microbiome

Microbial co-occurrence complicates associations of gut microbiome with US immigration, dietary intake and obesity – Wang et al. – Genome Biology

Signature changes in gut microbiome are associated with increased susceptibility to HIV-1 infection in MSM – Chen et al.  – Microbiome

Cognitive behavioral therapy for irritable bowel syndrome induces bidirectional alterations in the brain-gut-microbiome axis associated with gastrointestinal symptom improvement – Jacobs et al. – Microbiome. 

Human oral microbiome

Impact of sleep on the microbiome of oral biofilms – Sotozono et al. – PLOS One

Functional screening of a human saliva metagenomic DNA reveal novel resistance genes against sodium hypochlorite and chlorhexidine – Wigand et al. BMC Oral Health

Animal Experiments

The immunotoxicity, but not anti-tumor efficacy, of anti-CD40 and anti-CD137 immunotherapies is dependent on the gut microbiota – Blake et al. – Cell Reports Medicine

Colonization of gut microbiota by plasmid-carrying bacteria is facilitated by evolutionary adaptation to antibiotic treatment – Zhang et al. – ISME

Sexual dimorphism in glucose metabolism is shaped by androgen-driven gut microbiome – Gao et al. – Nature Communications