Category Archives: Plant Root Soil microbiome

February 28, 2022

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Human and General Microbiome

Fusobacterium nucleatum promotes colorectal cancer cells adhesion to endothelial cells and facilitates extravasation and metastasis by inducing ALPK1/NF-κB/ICAM1 axis – Ying Zhang – Gut Microbes

Oral and Intestinal Bacterial Substances Associated with Disease Activities in Patients with Rheumatoid Arthritis: A Cross-Sectional Clinical Study – Kaori Kitamura – Journal of Immunology Research

Cervicovaginal Microbiota Predicts Neisseria gonorrhoeae Clinical Presentation – Angela Lovett – Frontiers in Microbiology

Gut microbiota from Mexican patients with metabolic syndrome and HIV infection: an inflammatory profile – Fernando Amador-Lara – Journal of Applied Microbiology

Dysbiosis of skin microbiome and gut microbiome in melanoma progression – Chahrazed Mekadim – BMC Microbiology

Whole Genome Analysis of 335 New Bacterial Species from Human Microbiota Reveals a Huge Reservoir of Transferable Antibiotic Resistance Determinants – Sami Khabthani – International Journal of Molecular Sciences

Dynamics of the Gut Bacteria and Fungi Accompanying Low-Carbohydrate Diet-Induced Weight Loss in Overweight and Obese Adults – Dan Yu – Frontiers in Nutrition

The Gut Microbiome as a Biomarker of Cancer Progression Among Female Never-smokers With Lung Adenocarcinoma – Takehiro Otoshi – Anticancer Research

Impact Of The Ileal Microbiota On Surgical Site Infections In Crohn’s Disease: A Nationwide Prospective Cohort – Clément Julien – Journal of Crohn’s & Colitis

A multiple-dimension model for microbiota of patients with colorectal cancer from normal participants and other intestinal disorders – Jian Shen – Applied Microbiology and Biotechnology

Gut Microbiota Regulate Pancreatic Growth, Exocrine Function and Gut Hormones – Khyati Girdhar – Diabetes

Respiratory dysfunction three months after severe COVID-19 is associated with gut microbiota alterations – Beate Vestad – Journal of Internal Medicine

Gut microbiota and BMI throughout childhood: the role of firmicutes, bacteroidetes, and short-chain fatty acid producers – Timothy A Houtman – Scientific Reports

Review: Cross-reactivity between microbial and tumor antigens – Laurence Zitvogel – Current Opinion in Immunology

Review: The role of nutrition in inflammaging – Paolo Di Giosia – Ageing Research Reviews

Review: Impact of antibiotics on the human microbiome and consequences for host health – Dhrati V Patangia – MicrobiologyOpen

Beneficial Microbes and Compounds

Randomized, Double-blind, Placebo-controlled Study to Assess the Effect of Two Probiotics on the Preterms’ Gut Microbiota – Bárbara Moreno-Sanz – Journal of Pediatric Gastroenterology and Nutrition

Streptococcus strain C17(T) as a potential probiotic candidate to modulate oral health – Wen Xiao Zhang – Letters in Applied Microbiology

Animal Microbiome

Antimicrobial resistance profile of gram-positive isolates belonging to the microbiota of non-human primates – Melissa M Zaniolo – Journal of Medical Primatology

Gut microbiota differences between paired intestinal wall and digesta samples in three small species of fish – Lasse Nyholm – PeerJ

An experimental test of disease resistance function in the skin-associated bacterial communities of three tropical amphibian species – Myra C Hughey – FEMS Microbiology Ecology

Gut Microbiome Characteristics in feral and domesticated horses from different geographic locations – Li Ang – Communications Biology

Plant Microbiome

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

Changes in root microbiome during wheat evolution – Somayeh Gholizadeh – BMC Microbiology

Plant organ and sampling time point determine the taxonomic structure of microbial communities associated to apple plants in the orchard environment – Claudia Maria Oliveira Longa – Microbiological Research

Commensal Pseudomonas strains facilitate protective response against pathogens in the host plant – Or Shalev – Nature Ecology & Evolution

Review: Major Biological Control Strategies for Plant Pathogens – Manisha Arora Pandit – Pathogens

Bioinformatics

ADDAGMA: A database for domestic animal gut microbiome atlas – Yueren Xu – Computational and Structural Biotechnology Journal

To rarefy or not to rarefy: robustness and efficiency trade-offs of rarefying microbiome data – Johnny Hong – Bioinformatics

Techniques

Human Stool Preservation Impacts Taxonomic Profiles in 16S Metagenomics Studies – Anne Plauzolles – Frontiers in Cellular and Infection Microbiology

February 16, 2022

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Happy Wednesday! Today’s digest includes two gut-brain axis papers from Sarkis Mazmanian’s lab at CalTech. The first article, published in Nature, found that 4-ethylphenol (4EPS) produced by gut microbes from dietary tyrosine was capable of entering the brain and changing gene expression, brain cell interactions, and brain functions. In the second study, published in Nature Medicine, oral administration of the adsorbent AB-2004–which can bind and sequester phenolic compounds–led to reduced levels of gut 4EPS and decreased anxiety in human adolescents with autism spectrum disorder.

I have also included an article published by my thesis lab in The Journal of Allergy and Clinical Immunology looking at the impact of seasons on the respiratory microbiome and asthma exacerbations in children.

Finally, there is an interesting paper by Baranova et al. in which the authors identify a bacterial species ubiquitous across multiple wild animals that appears to have novel functions for pathogen control or microbiome remodeling. Happy reading!

General Microbiome
Scale-dependent tipping points of bacterial colonization resistance. – Karita, Y. et al., PNAS.

Microbial protection favors parasite tolerance and alters host-parasite coevolutionary dynamics. – Rafaluk-Mohr, C. et al., Current Biology.

Human Respiratory Microbiome
Seasonal Airway Microbiome and Transcriptome Interactions Promote Childhood Asthma Exacerbations. – McCauley, K.E. et al., The Journal of Allergy and Clinical Immunology.

Human Skin Microbiome
Secreted Toxins From Staphylococcus aureus Strains Isolated From Keratinocyte Skin Cancers Mediate Pro-tumorigenic Inflammatory Responses in the Skin. – Krueger, A. et al., Frontiers in Microbiology.

Aged related human skin microbiome and mycobiome in Korean women. – Kim, H-J. et al., Scientific Reports.

Human Vaginal Microbiome
Extracellular Vesicles Generated by Gram-Positive Bacteria Protect Human Tissues Ex Vivo From HIV-1 Infection. – Costantini, P.E. et al., Frontiers in Cellular and Infection Microbiology.

Gut-Brain Axis
A gut-derived metabolite alters brain activity and anxiety behavior in mice. – Needham, B.D. et al., Nature.

Safety and target engagement of an oral small-molecule sequestrant in adolescents with autism spectrum disorder: an open-label phase 1b/2a trial. – Campbell, A.S., Needham, B.D., Meyers, C.R. et al., Nature Medicine.

Animal Experiments
Tryptophan-derived microbial metabolites activate the aryl hydrocarbon receptor in tumor-associated macrophages to suppress anti-tumor immunity. – Hezaveh, K. et al., Immunity.

Stochastic microbiome assembly depends on context. – Jones, E.W. et al., PNAS.

IBD-Associated Atg16L1T300A Polymorphism Regulates Commensal Microbiota of the Intestine. – Liu, H. et al., Frontiers in Immunology.

A homeostatic interferon-lambda response to bacterial microbiota stimulates preemptive antiviral defense within discrete pockets of intestinal epithelium. – Van Winkle, J.A. et al. eLife.

Enteric nervous system modulation of luminal pH modifies the microbial environment to promote intestinal health. – Hamilton, M.K. et al., PLoS Pathogens.

Animal Microbiome
Characterization of the Gut Microbiome and Resistomes of Wild and Zoo-Captive Macaques. – Jia, T. et al., Frontiers in Veterinary Science.

Deep Functional Profiling of Wild Animal Microbiomes Reveals Probiotic Bacillus pumilus Strains with a Common Biosynthetic Fingerprint. – Baranova, M.N. et al., International Journal of Molecular Sciences.

Plant, Root, and Soil Microbiome
Plant immunity suppression via PHR1-RALF-FERONIA shapes the root microbiome to alleviate phosphate starvation. – Tang, J. et al., The EMBO Journal.

Extracts from Environmental Strains of Pseudomonas spp. Effectively Control Fungal Plant Diseases. – Librizzi, V. et al., Plants.

Mega-fire in Redwood Tanoak Forest Reduces Bacterial and Fungal Richness and Selects for Pyrophilous Taxa that are Phylogenetically Conserved. – Enright, D.J. et al., Molecular Ecology.

Water and Extremophile Microbiome
Analysis of antibiotic resistance genes reveals its important role in influencing the community structure of ocean microbiome. – Yang, P. et al., The Science of the Total Environment.

Seaweeds influence oyster microbiota and disease susceptibility. – Dugeny, E. et al., The Journal of Animal Ecology.

Air Microbiome
Vertical stratification of the air microbiome in the lower troposphere. – Drautz-Moses, D.I. et al., PNAS.

Bioinformatics
Evaluating supervised and unsupervised background noise correction in human gut microbiome data. – Briscoe, L. et al., PLoS Computational Biology.

February 9, 2022

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Today’s digest includes a Nature Medicine news feature on the role of preprints in the COVID-19 pandemic. Also included are an article about unsupervised clustering methods for microbiome data, the response of anammox consortia to nutrient starvation, and a handful of interesting preprints.

Animal experiments

Preprint: Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig – Gaio et al. – bioRxiv

Plant, root, and soil microbiome

Preprint: Ecological insights into soil health according to the life-history traits and environment-wide associations of bacteria in agricultural soils – Wilhelm et al. – bioRxiv

Water and extremophile microbiome

Response and resilience of anammox consortia to nutrient starvation – Wang et al. – Microbiome

Bioinformatics

Preprint: Model-free prediction of microbiome compositions – Asher & Bashan – bioRxiv

Preprint: Predicting the re-distribution of antibiotic molecules caused by inter-species interactions in microbial communities – Reding – bioRxiv

Performance determinants of unsupervised clustering methods for microbiome data – Shi et al. – Microbiome

Science, publishing, and career

Rise of the preprint: how rapid data sharing during COVID-19 has changed science forever – Watson – Nature Medicine

February 4, 2022

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Today’s digest is super diverse (read cool!): novel genes from uncultivated prokaryotes, a new Latilactobacillus species isolated from leaves of a strawberry plant (read the full 🍓 story behind the paper!), the benchmarking study of taxonomic profilers for long-read shotgun metagenomic datasets, and more. The first Issue of a new international peer-reviewed, open access, microbiome-oriented journal – the Microbiome Research Reports – is out with one original article, one perspective and four reviews.
And, a bit of shameless self-promotion, check out my preprint on urinary microbiome of healthy European women!
Happy Friday!

Global microbiome

*Functional and evolutionary significance of unknown genes from uncultivated taxa – Alvaro Rodríguez – bioRxiv

Ear microbiome

The adult microbiome of healthy and otitis patients: Definition of the core healthy and diseased ear microbiomes – Maria Burton – PlosOne

Respiratory microbiome

Intestinal Akkermansia muciniphila predicts clinical response to PD-1 blockade in patients with advanced non-small-cell lung cancer – Lisa Derosa – Nature Medicine

Associations and recovery dynamics of the nasopharyngeal microbiota during influenza‑like illness in the aging population – Sudarshan A. Shetty – Scientific Reports

Genomic diversity and antimicrobial resistance of Prevotella species isolated from chronic lung disease airways – Kasey A. Webb – Microbial Genomics

Gut microbiome

Effect of host genetics on the gut microbiome in 7,738 participants of the Dutch Microbiome Project – Esteban A. Lopera-Maya – Nature Genetics


The gut bacterial community potentiates Clostridioides difficile infection severity – Nicholas A Lesniak – bioRxiv

Emergent evolutionary forces in spatial models of microbial growth in the human gut microbiota – Olivia M. Ghosh and Benjamin H. Good – bioRxiv

Review: Microbiome-based therapeutics – Matthew T. Sorbara and Eric G. Pamer – Nature Reviews Microbiology

Review: Multimodal interactions of drugs, natural compounds and pollutants with the gut microbiota –Anna E. Lindell – Nature Reviews Microbiology

Review: Gut microbiome and health: mechanistic insights – Willem M de Vos – Gut

Vaginal microbiome

Gardnerella vaginalis induces matrix metalloproteinases in the cervicovaginal epithelium through TLR-2 activation – Kristin D. Gerson – American Journal of Obstetrics & Gynecology/SMFM 42nd Annual Meeting: The Pregnancy Meeting

Urinary microbiome

*Extended bacterial diversity of the urinary microbiome of reproductive-age healthy European women captured by culturomics and long-read amplicon sequencing – Svetlana Ugarcina Perovic – bioRxiv

Phylogenetic analysis and antimicrobial susceptibility profile of uropathogens – Hanif Ullah – PlosOne

Multidrug-resistant Uro-associated Escherichia coli Populations and Recurrent Urinary Tract Infections in Patients Performing Clean Intermittent Self-catheterisation – Catherine Mowbray – European Urology Open Science

Plant microbiome

*Latilactobacillus fragifolii sp. nov., isolated from leaves of a strawberry plant (Fragaria x ananassa) – Marie Legein – International Journal of Systematic and Evolutionary Microbiology

Ecology and potential functions of plant-associated microbial communities in cold environments – Malek Marian – FEMS Microbiology Ecology

Animal microbiome

Gut microbiome of the largest living rodent harbors unprecedented enzymatic systems to degrade plant polysaccharides – Lucelia Cabral – Nature Communications

Review: Pesticide-induced disturbances of bee gut microbiotas – Michelle Z Hotchkiss – FEMS Microbiology Reviews

Animal experiments

Effect of a freeze-dried coffee solution in a high-fat diet-induced obesity model in rats: Impact on inflammatory response, lipid profile, and gut microbiota – Marilia Hermes Cavalcanti – PlosOne

Gut microbiota and butyrate contribute to nonalcoholic fatty liver disease in premenopause due to estrogen deficiency – Limin Liu – PlosOne

Techniques

BIOME-Preserve: A novel storage and transport medium for preserving anaerobic microbiota samples for culture recovery – Embriette R. Hyde – PlosOne

Species-targeted sorting and cultivation of commensal bacteria from the gut microbiome using flow cytometry under anaerobic conditions – Samuel Bellais – Microbiome

Bioinformatics

*Evaluation of taxonomic profiling methods for long-read shotgun metagenomic sequencing datasets – Daniel M Portik – bioRxiv

AGAMEMNON: an Accurate metaGenomics And MEtatranscriptoMics quaNtificatiON analysis suite – Giorgos Skoufos – Genome Biology

McComedy: A user-friendly tool for next-generation individual-based modeling of microbial consumer-resource systems – André Bogdanowski – Plos Computational Biology

VeChat: Correcting errors in long reads using variation graphs – Xiao Luo – bioRxiv

ReadBouncer: Precise and Scalable Adaptive Sampling for Nanopore Sequencing – Jens-Uwe Ulrich – bioRxiv

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January 26, 2022

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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 18, 2022

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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

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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

January 7, 2022

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Today’s digest covers a range of topics including a duplex qPCR assay to detect lung infections, an investigation into sand fly symbionts, and a characterization of a fermented soybean food (Pe poke). If you want to end the week on a good note, I’d suggest reading the two articles I’ve highlighted below. One demonstrates that flooding and ecological restoration of former cranberry farmland also restores wetland microbial communities and soil function. The second provides a new barcoding strategy for the phenotypic screening of mosquitos that can be applied towards malaria research.

Happy reading!

General microbiome

Controlled spatial organization of bacterial growth reveals key role of cell filamentation preceding Xylella fastidiosa biofilm formation – Anbumani et al. – npj Biofilms and Microbiomes

Bacteria can be selected to help beneficial plasmids spread – Dimitriu et al. – PLOS Biology

Genome-wide gene expression noise in Escherichia coli is condition-dependent and determined by propagation of noise through the regulatory network – Urchueguía et al. – PLOS Biology

Human respiratory microbiome

Detection of Pneumocystis jirovecii and Toxoplasma gondii in patients with lung infections by a duplex qPCR assay – Wu et al. – PLOS Neglected Tropical Diseases

Animal experiments

***Barcoded Asaia bacteria enable mosquito in vivo screens and identify novel systemic insecticides and inhibitors of malaria transmission – Sturm et al. – PLOS Biology

Molecular phylogeny of heritable symbionts and microbiota diversity analysis in phlebotominae sand flies and Culex nigripalpus from Colombia – Vivero-Gomez – PLOS Neglected Tropical Diseases

Plant, root, and soil microbiome

Shotgun sequence-based metataxonomic and predictive functional profiles of Pe poke, a naturally fermented soybean food of Myanmar – Tamang et al. – PLOS One

***Flooding and ecological restoration promote wetland microbial communities and soil functions on former cranberry farmland – Rubin et al. – PLOS One

Water and extremophile microbiome

Coral reef biofilm bacterial diversity and successional trajectories are structured by reef benthic organisms and shift under chronic nutrient enrichment – Remple et al. – npj Biofilms and Microbiomes

January 6, 2022

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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

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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