Author Archives: Axel Künstner

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 08, 2021

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General microbiome

Clinical medicine journals lag behind science journals with regards to “microbiota sequence” data availability – Pryor et al. – Clinical and Translational Medicine

Role of the Microbiome in Regulating Bone Metabolism and Susceptibility to Osteoporosis – Cronin et al. – Calcified Tissue International

Defining and quantifying the core microbiome: Challenges and prospects – Neu, Allen & Roy – PNAS

Clean room microbiome complexity impacts planetary protection bioburden – Hendrickson et al. – Microbiome

[PREPRINT]Community Composition of Bacteria Isolated from Swiss Banknotes Varies Depending on Collection Environment – Bischofberger & Hall – bioRxiv

Microbiota and stress: a loop that impacts memory – Kraimi et al. – Psychoneuroendocrinology

Species- and site-specific genome editing in complex bacterial communities – Rubin et al. – Nature Microbiology

Human respiratory microbiome

Integrated metabolic and microbial analysis reveals host–microbial interactions in IgE-mediated childhood asthma – Chiu et al. – Scientific Reports

Human oral microbiome

Metagenome-genome-wide association studies reveal human genetic impact on the oral microbiome – Liu et al. – Cell Discovery

Human gut microbiome

Interaction Between Intestinal Microbiota, Immunology Molecular Mimicry, and AID – Pan et al. – Journal of Immunology Research

[REVIEW]The Gut Microbiome and Hepatocellular Carcinoma – Akkiz – Journal of Gastrointestinal Cancel

Anaerostipes hominis sp. nov., a novel butyrate-producing bacteria isolated from faeces of a patient with Crohn’s disease – Lee et al. – International Journal of Systematic and Evolutionary Microbiology

Gut microbiome is associated with the clinical response to anti-PD-1 based immunotherapy in hepatobiliary cancers – Mao et al. – Journal for ImmunoTherapy of Cancer

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

Time-restricted feeding induces Lactobacillus- and Akkermansia-specific functional changes in the rat fecal microbiota – Palomba et al. – NPJ Biofilms and Microbiomes

Animal microbiome (for animals in the wild)

Diet-driven mercury contamination is associated with polar bear gut microbiota – Watson et al. – Scientific Reports

Maternal inheritance of the koala gut microbiome and its compositional and functional maturation during juvenile development – Blyton et al. – Environmental Microbiology

[PREPRINT]Relationships between pond water and tilapia skin microbiomes in aquaculture ponds in Malawi – McMurtie et al. – bioRxiv

Age-Based Variations in the Gut Microbiome of the Shennongjia (Hubei) Golden Snub-Nosed Monkey (Rhinopithecus roxellana hubeiensis) – Yao et al. – BioMed Research International

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

Looking through the FOG: microbiome characterization and lipolytic bacteria isolation from a fatberg site – Court et al. – Microbiology

The Baltic Sea methane pockmark microbiome: The new insights into the patterns of relative abundance and ANME niche separation – Iasakov et al. – Marine Environmental Research

Bioinformatics

3MCor: an integrative web server for metabolome-microbiome-metadata correlation analysis – Sun et al. – Bioinformatics

Techniques

Microbiome Methods in Experimental Autoimmune Encephalomyelitis – Daberkow et al. – Current Protocols

[PREPRINT]A wipe-based stool collection and preservation kit for microbiome community profiling – Hua et al. – bioRxiv

December 01, 2021

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General microbiome

Searching for New Microbiome-Targeted Therapeutics through a Drug Repurposing Approach – Barone et al. – Journal of Medicinal Chemistry

Current status of intratumour microbiome in cancer and engineered exogenous microbiota as a promising therapeutic strategy – Chen et al. – Biomedicine & Pharmacotherapy

Regulation of blood–brain barrier integrity by microbiome-associated methylamines and cognition by trimethylamine N-oxide – Hoyles et al. – Microbiome

Modeling host-associating microbes under selection – Bansept et al. – The ISME Journal

Human oral microbiome

Bacterial variation in the oral microbiota in multiple sclerosis patients – Zangeneh – PLOS One

Human gut microbiome

[REVIEW]Gut microbiota as a transducer of dietary cues to regulate host circadian rhythms and metabolism – Choi, Rao & Chang – Nature Reviews Gastroenterology & Hepatology

[REVIEW]Gut microbiota-derived short-chain fatty acids and colorectal cancer: Ready for clinical translation? – Hou et al. – Cancer Letters

Analysis of changes in microbiome compositions related to the prognosis of colorectal cancer patients based on tissue-derived 16S rRNA sequences – Coi et al. – Journal of Translational Medicine

The Fecal Microbiome and Metabolome of Pitt Hopkins Syndrome, a Severe Autism Spectrum Disorder – Dilmore et al. – mSystems

Characterization of gut microbial structural variations as determinants of human bile acid metabolism – Wang et al. – Cell Host & Microbe

Animal microbiome

Microbial regulation of hexokinase 2 links mitochondrial metabolism and cell death in colitis – Hinrichsen et al. – Cell Metabolism

Bacterial communities from vagina of dairy healthy heifers and cows with impaired reproductive performance – Moreno et al. – Research in Veterinary Science

Plant, root, and soil microbiome

Artificial Selection on Microbiomes To Breed Microbiomes That Confer Salt Tolerance to Plants – Mueller et al. – mSystems

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations – ter Horst et al. – Microbiome

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

Degradation of biological macromolecules supports uncultured microbial populations in Guaymas Basin hydrothermal sediments – Castro et al. – The ISME Journal

Microbial community structure in hadal sediments: high similarity along trench axes and strong changes along redox gradients – Schauberger et al. – The ISME Journal

Bioinformatics

Disentangling environmental effects in microbial association networks – Deutschmann et al. – Microbiome

Negative Binomial factor regression with application to microbiome data analysis – Muller, Mishra

Techniques

Novel clades of soil biphenyl degraders revealed by integrating isotope probing, multi-omics, and single-cell analyses – Chen et al. – The ISME Journal

November 26, 2021

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General microbiome

Metabolomics-Microbiome Crosstalk in the Breast Cancer Microenvironment – Al-Ansari – Metabolites

Aspergillus fumigatus pan-genome analysis identifies genetic variants associated with human infection – Barber et al. – Nature Microbiology

Human gut microbiome

Human gut bacterial metabolism drives Th17 activation and colitis – Alexander et al. – Cell Host & Microbiome

Integrative Analysis of Metabolome and Microbiome in Patients with Progressive Alcohol-Associated Liver Disease – Gao et al. – Metabolites

Human Fecal Metabolome Reflects Differences in Body Mass Index, Physical Fitness, and Blood Lipoproteins in Healthy Older Adults – Cui et al. – Metabolites

[REVIEW]Gut Microbiota, Microbial Metabolites and Human Physical Performance – Lensu & Pekkala – Metabolites

[Editorial]Next steps after 15 stimulating years of human gut microbiome research – Clavel et al. – Microbial Biotechnology

[REVIEW]The microbiome, Gastrointestinal cancer and immunotherapy – Newsome, Yang & Jobin – Journal of Gastroenterology and Hepatology

Mycobiota-induced IgA antibodies regulate fungal commensalism in the gut and are dysregulated in Crohn’s disease – Doron et al. – Nature Microbiology

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

Fecal microbiota transplantation protects rotenone-induced Parkinson’s disease mice via suppressing inflammation mediated by the lipopolysaccharide-TLR4 signaling pathway through the microbiota-gut-brain axis – Zhao et al. – Microbiome

Xylan alleviates dietary fiber deprivation-induced dysbiosis by selectively promoting Bifidobacterium pseudocatenulatum in pigs – Wang et al. Microbiome

Animal microbiome (for animals in the wild)

Circadian dynamics of the teleost skin immune-microbiome interface – Ellison, Wilcockson & Cable – Microbiome

Honey bee genetics shape the strain-level structure of gut microbiota in social transmission – Wu et al. – Microbiome

Plant, root, and soil microbiome

Evidence for host–microbiome co-evolution in apple – Abdelfattah et al. – New Phytologist

Protective role of the Arabidopsis leaf microbiota against a bacterial pathogen – Vogel et al. – Nature Microbiology

Emergent bacterial community properties induce enhanced drought tolerance in Arabidopsis – Yang et al. – npj Biofilms and Microbiomes

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

Cross-regional scale pollution of freshwater biofilms unveiled by antibiotic resistance genes – Yao et al. – Science of The Total Environment

Functional metagenomic analysis of quorum sensing signaling in a nitrifying community – Tan et al. – npj Biofilms and Microbiomes

Bioinformatics

Multivariable association discovery in population-scale meta-omics studies – Mallick et al. – PLOS Computational Biology

Techniques

Assessing saliva microbiome collection and processing methods – Armstrong, Parmar & Blaser – npj Biofilms and Microbiomes

November 17, 2021

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General microbiome

Macrophages in Microbial Pathogenesis: Commonalities of Defense Evasion Mechanisms – Pandey et al. – Infection and Immunity

Human respiratory microbiome

The Influence of FUT2 and FUT3 Polymorphisms and Nasopharyngeal Microbiome on Respiratory Infections in Breastfed Bangladeshi Infants from the Microbiota and Health Study – Binia et al. – mSphere

Human gut microbiome

Fecal Microbiota Transplantation Commonly Failed in Children with Co-Morbidities – Kellermayer et al. – JPGN

Current and future applications of fecal microbiota transplantation for children – Chen & Chiu – Biomedical Journal

[REVIEW]Microbial influences on gut development and gut-brain communication – Ye & Rawls – Development

Characterization and predictive functional profiles on metagenomic 16S rRNA data of liver transplant recipients: A longitudinal study – Sivaraj et al. – Clinical Transplantation

Changes to human faecal microbiota after international travel – Kampmann et al. – Travel Medicine and Infectious Disease

Animal experiments

Cognate recognition of microbial antigens defines constricted CD4+ T cell receptor repertoires in the inflamed colon – Muschaweck et al. – Immunity

An aniline-substituted bile salt analog protects both mice and hamsters from multiple Clostridioides difficile strains – Phan et al. – Antimicrobial Agents and Chemotherapy

Analysis of Cow-Calf Microbiome Transfer Routes and Microbiome Diversity in the Newborn Holstein Dairy Calf Hindgut – Zhu et al. – Frontiers in Nutrition

Metabolome

Multi-omic evaluation of metabolic alterations in multiple sclerosis identifies shifts in aromatic amino acid metabolism – Fitzgerald et al. – Cell Reports Medicine

Bioinformatics

[REVIEW]It takes guts to learn: machine learning techniques for disease detection from the gut microbiome – Curry, Nute & Treangen – Emerging Topics in Life Sciences

November 10, 2021

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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

October 27, 2021

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COVID19

Severe dysbiosis and specific Haemophilus and Neisseria signatures as hallmarks of the oropharyngeal microbiome in critically ill COVID-19 patients – de Castilhos et al – Clinical Infectious Diseases

General microbiome

The Role of Microbiota in Infant Health: From Early Life to Adulthood – Yao et al. – Front. Immunol.

The microbiome impacts host hybridization and speciation – Miller et al. – PLOS Biology

Pregnancy and early life

Gut Dysbiosis, Bacterial Colonization and Translocation, and Neonatal Sepsis in Very-Low-Birth-Weight Preterm Infants – Lee et al. – Front. Microbiol.

Multi-site human microbiome

Oral, nasal, and gut microbiota in Parkinson’s disease – Li et al. – Neuroscience

Human respiratory microbiome

[REVIEW]Emerging cellular and molecular interactions between the lung microbiota and lung diseases – Xiang & Meng – Critical Reviews in Microbiology

Human gut microbiome/mycobiome

[REVIEW]Drugs and Bugs: The Gut-Brain Axis and Substance Use Disorders – Simpson et al. – Journal of Neuroimmune Pharmacology

Metagenomic analysis reveals the signature of gut microbiota associated with human chronotypes – Carasso et al. – The FASEB Journal

Intestinal mycobiota composition and changes in children with thalassemia who underwent allogeneic hematopoietic stem cell transplantation – Yalcin et al. – Pediatric Blodd & Cancer

Gut microbiota analyses of Saudi populations for type 2 diabetes-related phenotypes reveals significant association – AlAli et al. – bioRxiv

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

Consistent gut bacterial and short-chain fatty acid signatures in hypoabsorptive bariatric surgeries correlate with metabolic benefits in rats – Mukorako et al. – International Journal of Obesity

Microbiota instruct IL-17A-producing innate lymphoid cells to promote skin inflammation in cutaneous leishmaniasis – Singh et al – PLOS Pathogens

Anti-inflammatory effects of purple sweet potato anthocyanin extract in DSS-induced colitis: modulation of commensal bacteria and attenuated bacterial intestinal infection – Mu et al. – Food & Function

Plant, root, and soil microbiome/virome

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil – Trubl et al. – Microbiome

Arabidopsis assemble distinct root-associated microbiomes through the synthesis of an array of defense metabolites – Kudjordjie, Sapkota & Nicolaisen – PLOS One

Microbiome of Pukzing Cave in India shows high antimicrobial activity against plant and animal pathogens – Iquebal et al. – Genomics

[REVIEW]Phyllosphere microbiome: Diversity and functions – Bashir et al. – Microbiological Research

[REVIEW]Rhizospheric microbiome: Bio-based emerging strategies for sustainable agriculture development and future perspectives – Kumawat, Razdan & Saharan – Microbiological Research

Phages and viruses

[REVIEW]The intestinal virome: lessons from animal models – Chaffringeon et al. – Current Opinion in Virology

Bioinformatics

[REVIEW]Application of Deep Learning in Plant–Microbiota Association Analysis – Deng et al. – Frontiers in Genetics

Techniques

Simple solution to preserve plant samples for microbiome analyses – Carvalhais et al. – Molecular Ecology Resources

[REVIEW]Novel methods of microbiome analysis in the food industry – Sabater et al. – nternational Microbiology

October 20, 2021

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General microbiome

[REVIEW]Controlled Complexity: Optimized Systems to Study the Role of the Gut Microbiome in Host Physiology – Glowacki, Engelhart & Ahern – Frontiers in Microbiology

[REVIEW]Microbiota-brain interactions: Moving toward mechanisms in model organisms – Nagpal & Cryan – Neuron

Functional attractors in microbial community assembly – Estrela et al. – Cell Systems

Bloodstream infections’ origins following fecal microbiota transplantation: a strain- level analysis – Eshel et al. – Blood Advances

Probiotic consumption influences universal adaptive mutations in indigenous human and mouse gut microbiota – Ma et al. – Communications Biology

Multi-site human microbiome

[PREPRINT]Obesity influences composition of salivary and fecal microbiota and impacts the interactions between bacterial taxa – Bombin et al. – bioRxiv

Human vaginal microbiome

Does probiotics work for bacterial vaginosis and vulvovaginal candidiasis – Han & Ren – Current Opinion in Pharmacology

Human gut microbiome

A meta-analysis study of the robustness and universality of gut microbiome-metabolome associations – Muller, Algavi & Borenstein – Microbiome

Specific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance – de Filippis et al. – Nature Communications

Drinking Water Source and Intake Are Associated with Distinct Gut Microbiota Signatures in US and UK Populations – Vanhaecke et al. – The Journal of Nutrition

The Gut Microbiota during a Behavioral Weight Loss Intervention – Stanislawski et al. – Nutrients

Effect of chewing betel nut on the gut microbiota of Hainanese – Ying et al. – PLOS One

[PREPRINT]Codiversification of gut microbiota with humans – Suzuki et al. – bioRxiv

Response to PD-1-Based Immunotherapy for Non-Small Cell Lung Cancer Altered by Gut Microbiota – He et al. – Oncology and Therapy

Human metabolome

Changes in serum and urinary metabolomic profile after a dietary intervention in patients with irritable bowel syndrome – Nybacka et al. – PLOS One

The influence of the gut microbiome on BCG-induced trained immunity – Strazar et al. – Genome Biology

Animal microbiome

Weaning age and its effect on the development of the swine gut microbiome and resistome – Holman et at. – bioRxiv

Sandalwood seed oil improves insulin sensitivity in high-fat/high-sucrose diet-fed rats associated with altered intestinal microbiota and its metabolites – Gao et al. – Food & Function

Plant, root, and soil microbiome

Active virus-host interactions at sub-freezing temperatures in Arctic peat soil – Trubl et al. – Microbiome

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

PREPRINT[]Bacterial, phytoplankton, and viral dynamics of meromictic Lake Cadagno offer insights into the Proterozoic ocean microbial loop – Saini et al. – bioRxiv

Metagenomic analysis provides functional insights into seasonal change of a non-cyanobacterial prokaryotic community in temperate coastal waters – Matsumoto et al. – PLOS One

[PREPRINT]Survival of hatchery grown native oysters is associated with specific gut-associated bacteria at various locations within the Puget Sound – Kunselmann et al. – bioRxiv

Built environment (subways, indoor surfaces)

Microbial colonization and resistome dynamics in food processing environments of a newly opened pork cutting industry during 1.5 years of activity – Cobo-Diaz et al. – Microbiome

Food microbiology

Effects of ultrasound treatments on wine microorganisms – Munoz et al. – Ultrasonics Sonochemistry

Effect of roasting conditions on cocoa bioactivity and gut microbiota modulation – Maldonado-Mateus et al. – Food & Function

Bioinformatics

[PREPRINT]Development of a metatranscriptomic analysis method for multiple intestinal sites and its application to the common marmoset intestine – Uehara et al. – bioRxiv

Recovery of strain-resolved genomes from human microbiome through an integration framework of single-cell genomics and metagenomics – Arikawa et al. – Microbiome

[PREPRINT]Metagenome assembly of high-fidelity long reads with hifiasm-meta – Feng et al. – arXiv.org

Fast and Accurate Distance-based Phylogenetic Placement using Divide and Conquer – Balaban et al. – Molecular Ecology Resources

Microbes in the news (popular press, EurekAlert, ScienceDaily, Youtube, NPR, etc)

Should You Get a Microbiome Test? – Anahad O’Connor – New York Times