Tag Archives: Microbiome Digest

September 16, 2020

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Greetings from Chile! Today, in this Digest, it is worth to highlight: a study showing associations between the use of antibiotics and the risk of appendicitis, a review about microbiota and colorectal cancer (CRC) risk and another review about markers for diabetes-associated chronic kidney disease. In addition, there are a set of papers about microbiome changes under short- and long-term antibiotic use in the animal lab, and microbiota changes in the treatment of non-model animals, such as the sika deer.   

Human Microbiome

Antibiotics during childhood and development of appendicitis-a nationwide cohort study – Jacob Antonsen – Alimentary Pharmacology and Therapeutics

Review: Bacteria-related changes in host DNA methylation and the risk for CRC – Iradj Sobhani – Gut Microbes

Review: Potential for Novel Biomarkers in Diabetes-Associated Chronic Kidney Disease: Epigenome, Metabolome, and Gut Microbiome – Ashani Lecamwasam – Biomedicines

Microbiota-Mitochondria Inter-Talk: A Potential Therapeutic Strategy in Obesity and Type 2 Diabetes – Teresa Vezza – Antioxidants

Preprint: Impact of sleep fragmentation, heart failure, and their combination, on the gut microbiome – Olfat Khannous-Lleiffe – BioRxiv

Microbiome and Diet

Relative abundance of the Prevotella genus within the human gut microbiota of elderly volunteers determines the inter-individual responses to dietary supplementation with wheat bran arabinoxylan-oligosaccharides – Wing Sun Faith Chung – BMC Microbiology

Animal Microbiome

Acute and long-term effects of antibiotics commonly used in laboratory animal medicine on the fecal microbiota – Scott W. Korte – Veterinary Research

The impact of anthelmintic treatment on gut bacterial and fungal communities in diagnosed parasite-free sika deer Cervus nippon – Xiaolong Hu – Applied genetics and molecular biotechnology

On the way to specificity – Microbiome reflects sponge genetic cluster primarily in highly structured populations – Cristina Díez‐Vives – Molecular Ecology

The gut microbiota may be a novel pathogenic mechanism in loosening of orthopedic implants in rats – Meghan M. Moran – The FASEB Journal

Characterization of Gut Microbiota in Prenatal Cold Stress Offspring Rats by 16S rRNA Sequencing – Jiasan Zheng – Animals

Obesity Worsens Gulf War Illness Symptom Persistence Pathology by Linking Altered Gut Microbiome Species to Long-Term Gastrointestinal, Hepatic, and Neuronal Inflammation in a Mouse Model – Dipro Bose – Nutrients

Beneficial Microbes and Compounds

Influence of a cholesterol-lowering strain Lactobacillus plantarum LP3 isolated from traditional fermented yak milk on gut bacterial microbiota and metabolome of rats fed with a high-fat diet – Zitong Ding – Food and Function

The Microbiota-Derived Metabolite of Quercetin, 3,4-Dihydroxyphenylacetic Acid Prevents Malignant Transformation and Mitochondrial Dysfunction Induced by Hemin in Colon Cancer and Normal Colon Epithelia Cell Lines – Mabel Catalán – Molecules

Bioinformatics

Constructing bi-plots for random forest: Tutorial – Lionel Blanchet – Analytica Chimica Acta

More Microbes

Cultural isolation of spore-forming bacteria in human feces using bile acids – Masaru Tanaka – Scientific Reports

Bed bugs shape the indoor microbial community composition of infested homes – Madhavi L. Kakumanu – Science of The Total Environment

September 5, 2020

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Have a nice weekend! Today, this Digest includes a good amount of reviews covering different topics (from the concept of inflammageing to the impact of the microbiome on cancer treatment), as well as a report covering the use of flow cytometry to search for microbiome markers in Crohn’s disease patients, and studies on microbiota and portal hypertension, the microbiome of pesticide-treated soils and the effect of natural microbes on hydrocarbon degradation.

Human and General Microbiome

Cytometric fingerprints of gut microbiota predict Crohn’s disease state –  Peter Rubbens – The ISME Journal

Review: Is inflammageing influenced by the microbiota in the aged gut? A systematic review – Cabirou M Shintouo – Experimental Gerontology

Review: The Gut Microbiome, Inflammation, and Salt-Sensitive Hypertension – Fernando Elijovich – Current Hypertension Reports 

Review: Intestinal microbial metabolites in human metabolism and type 2 diabetes – Hilde Herrema – Diabetologia

Review: Gut Microbiota Dysbiosis as a Target for Improved Post-Surgical Outcomes and Improved Patient Care. A Review of Current Literature – Fatema Mustansir Dawoodbhoy – Shock

Review: The Role of the Microbiome in Cancer and Therapy Efficacy: Focus on Lung Cancer – Adrienne Halley – Anticancer Research 

Review: Breast and Gut Microbiota Action Mechanisms in Breast Cancer Pathogenesis and Treatment – Cancers (MDPI)

Review: Influence of Resveratrol on the Cardiovascular Health Effects of Chronic Kidney Disease – International Journal of Molecular Sciences

Review: An RNA-centric view on gut Bacteroidetes – Daniel Ryan – Biological Chemistry

Exploratory Research on the Relationship between Human Gut Microbiota and Portal Hypertension – Keiji Yokoyama – Internal Medicine

Gut microbiome alterations in type 1 autoimmune pancreatitis after induction of remission by prednisolone – Ken Kamata – Clinical and Experimental Immunology

Type I IFNs and CD8 T cells increase intestinal barrier permeability after chronic viral infection – Lara Labarta-Bajo – Journal of Experimental Medicine

Plant-associated Microbiome

Prokaryotic and microeukaryotic communities in an experimental rice plantation under long-term use of pesticides – Maria Pilar Serbent – 

Environmental Microbiome

Effect of natural microbiome and culturable biosurfactants-producing bacterial consortia of freshwater lake on petroleum-hydrocarbon degradation – Irfan Ali Phulpoto – Science of The Total Environment

Animal Microbiome

Alterations in the gut-associated microbiota of juvenile Caribbean spiny lobsters Panulirus argus (Latreille, 1804) infected with PaV1 – Jesús Alejandro Zamora-Briseño – Journal of Invertebrate Pathology

Effects of Zinc Oxide and Arginine on the Intestinal Microbiota and Immune Status of Weaned Pigs Subjected to High Ambient Temperature – Se Young Yoon – Animals (MDPI)

The Microbiome of Neotropical Water Striders and Its Potential Role in Codiversification – Anakena M Castillo – Insects (MDPI)

Beneficial Microbes and Compounds

Effects of probiotic bacterium Weissella cibaria CMU on periodontal health and microbiota: a randomised, double-blind, placebo-controlled trial – Mi-Sun Kang – BMC Oral Health

Other

A 500-year tale of co-evolution, adaptation, and virulence: Helicobacter pylori in the Americas – Zilia Y Muñoz-Ramirez – The ISME Journal

August 8, 2020

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Have a nice weekend, everyone! Today, in this Digest we have articles about the use of microbiome as markers of successful FMT for graft-versus-host disease treatment, as well as a set of papers about probiotics and different aspects of health, including an RCT in hypertensive women. In addition, other papers showing associations between microbiota and exposure to androgens in neonates, and a paper about the influence of the microablative fractional radiofrequency technique on microbiota of treated postmenopausal women.

Microbiome Research

Bacteroides fragilis is a potential marker of effective microbiota transplantation in acute graft-versus-host disease treatment – Oleg V. Goloshchapov – Cellular Therapy and Transplantation

Impact of microablative fractional radiofrequency on the vaginal health, microbiota, and cellularity of postmenopausal women – Ayane Cristine Sarmento – Clinics (Sao Paulo)

Gut Microbiota and Liver Interaction through Immune System Cross-Talk: A Comprehensive Review at the Time of the SARS-CoV-2 Pandemic – Emidio Scarpellini – Journal of Clinical Medicine

Neonatal exposure to androgens dynamically alters gut microbiota architecture – Alexia Barroso – Journal of Endocrinology

Environmental Microbiome

Physicochemical Parameters Affecting the Distribution and Diversity of the Water Column Microbial Community in the High-Altitude Andean Lake System of La Brava and La Punta – Reynaldo Núñez Salazar – Microorganisms

Preprint: Metabolic potential and survival strategies of microbial communities across extreme temperature gradients on Deception Island volcano, Antarctica – Amanda G Bendia – BioRxiv

Animal Models

Metagenomic insights into the effects of nanobubble water on the composition of gut microbiota in mice – Zitao Guo – Food and Function

Beneficial Microbes, Compounds, and Interventions

Effects of probiotic therapy on cardio-metabolic parameters and autonomic modulation in hypertensive women: a randomized, triple-blind, placebo-controlled trial – Larissa de Fátima Romão da Silva – Foods

Dietary Components, Microbial Metabolites and Human Health: Reading between the Lines – Yao Guo – Foods

Microbiota on Biotics: Probiotics, Prebiotics, and Synbiotics to Optimize Growth and Metabolism – Price T. Edwards – Gastrointestinal And Liver Physiology

The Effectiveness of Multi-Session FMT Treatment in Active Ulcerative Colitis Patients: A Pilot Study – Dorota Mańkowska-Wierzbicka – Biomedicines

Neurological and cognitive significance of probiotics: a holy grail deciding individual personality – Muhammad Afzal – Future Medicine

Bioinformatics and Genomics

The Influences of Bioinformatics Tools and Reference Databases in Analyzing the Human Oral Microbial Community – Maria A. Sierra  – Genes

Preprint: Genome-based targeted sequencing as a reproducible microbial community profiling assay – Jacquelynn Benjamino – BioRxiv

July 18, 2020

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Have a nice weekend! Today, in this Digest: microbiome in psoriasis, cancer and a set of papers about vaginal microbiome.  

Human and General Microbiome

The cutaneous and intestinal microbiome in psoriatic disease – Stephanie T. Lea – Clinical Immunology

Microbiome-induced antigen presenting cell recruitment coordinates skin and lung allergic inflammation – Niki D. Ubags – Journal of Allergy and Clinical Immunology

Butyrate, but not Propionate, Reverses Maternal Diet-Induced Neurocognitive Deficits in Offspring – Linchao Yu – Pharmacological Research

Host Genotype and Colonist Arrival Order Jointly Govern Plant Microbiome Composition and Function – Devin R. Leopold – Current Biology

Characterization of gut contractility and microbiota in patients with severe chronic constipation – Dina R. Yarullina – PLoS ONE

A high-resolution transcriptome map identifies small RNA regulation of metabolism in the gut microbe Bacteroides thetaiotaomicron – Daniel Ryan – Nature Communications 

Bacteria pathogens drive host colonic epithelial cell promoter hypermethylation of tumor suppressor genes in colorectal cancer – Xiaoxuan Xia – Microbiome

Vaginal microbiome analysis of healthy women during different periods of gestation – Dan Li – Bioscience Reports

The Gut Microbiome as a Component of the Gut-Brain Axis in Cognitive Health – Wen Gao – Biological Research For Nursing 

The Effect of Gut Microbiome on Carcinogenic DNA Damage – Yun-Chung Hsiao – Chemical Research in Toxicology

The effect of curative resection on fecal microbiota in patients with colorectal cancer: a prospective pilot study – Sung Sil Park – Annals of Surgical Treatment and Research

Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer – Travis T Sims – International Journal of Gynecological Cancer

Gut microbial composition changes in bladder cancer patients: A case-control study in Harbin, China – Canxia He –  Asia Pacific Journal of Clinical Nutrition

Beneficial Microbes, Interventions, and Compounds

A 4-strain Probiotic Supplement Influences Gut Microbiota Composition and Gut Wall Function in Patients with Ulcerative Colitis – Jonas Ghyselinck – International Journal of Pharmaceutics

Systematic Review: Probiotics for induction of remission in Crohn’s disease – Berkeley N Limketkai – Cochrane Systematic Review

Human milk and mucosa-associated disaccharides impact on cultured infant fecal microbiota – Antonio Rubio-del-Campo – Scientific Reports 

YYFZBJS ameliorates colorectal cancer progression in ApcMin/+ mice by remodeling gut microbiota and inhibiting regulatory T-cell generation – Hua Sui – Cell Communication and Signaling 

Challenges of Screening Prospective Stool Donors for Fecal Microbiota Transplantation – Nancy E. Dubois – Biological Research For Nursing

Effects of banana powder (Musa acuminata Colla) on the composition of human fecal microbiota and metabolic output using in vitro fermentation – Dan‐Dan Tian – Journal of Food Science

COVID-19 Papers

ACE2 and TMPRSS2 expression by clinical, HLA, immune, and microbial correlates across 34 human cancers and matched normal tissues: implications for SARS-CoV-2 COVID-19 – Riyue Bao – Journal of ImmunoTheraphy of Cancer

July 4, 2020

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Greetings from Santiago, Chile! Today in this Digest, we have studies about the influence of alcohol use disorder on the microbiota, several papers about the influence of different compounds (from allicin to DAV132, a colon-targeted antibiotic adsorbent) on the microbiota. Today we have several papers about different models of plant- or soil- associated microbiomes, and a couple of papers from studies with SIV infection models. Have a nice weekend!

Human and General Microbiome

Longitudinal gut microbiome changes in alcohol use disorder are influenced by abstinence and drinking quantity – Nancy Ames et al., – Gut Microbes

Comparative evaluation of peptidome and microbiota in different types of saliva samples – Ce Zhu et al., – Annals of Translational Medicine

Preprint: Microbial control over host diet selection – Brian K Trevelline and Kevin D Kohl – BioRxiv

Functional Compounds and the Microbiome

Hemolysin BL from novel Bacillus toyonensis BV-17 induces antitumor activity both in vitro and in vivo – Jiajia Chen et al., – Gut Microbes

Modeling the effect of DAV132, a novel colon-targeted adsorbent, on fecal concentrations of moxifloxacin and gut microbiota diversity in healthy volunteers – Jinju Guk et al., – Clinical Pharmacology and Therapeutics

Allicin-induced host-gut microbe interactions improves energy homeostasis – Chuanhai Zhang et al., – The FASEB Journal

Evidence of Microbiome-Drug Interactions between the Antimalarial Lumefantrine and Gut Microbiota in Mice – Matthew M. Ippolito et al., – The American Society of Tropical Medicine and Hygiene

Contrasting effects of viscous and particulate fibers on colonic fermentation in vitro and in vivo, and their impact on intestinal water studied by MRI in a randomized trial – David Gunn et al., – The American Journal of Clinical Nutrition

Animal Microbiome / Animal Models

A theoretic approach to the mode of gut microbiome translocation in SIV-infected Asian macaques – Wendy Li and Zhanshan (Sam) Ma – FEMS Microbiology Ecology

Impact of Initial Feeding and Molting on Tachypleus tridentatus Gut Microbiota – Fengze Miao et al., – Current Microbiology 

Osmotic stress induces gut microbiota community shift in fish – Keng Po Lai et al., – Environmental Microbiology

The Gut-Eye Axis: Lessons Learned from Murine Models – Jason L. Floyd & Maria B. Grant – Ophthalmology and Therapy 

The colonic mucosa-associated microbiome in SIV infection: shift towards Bacteroidetes coincides with mucosal CD4+ T cell depletion and enterocyte damage – Kristina Allers et al., – Scientific Reports  

Plant or Soil Microbiomes

Re-Analysis of 16S Amplicon Sequencing Data Reveals Soil Microbial Population Shifts in Rice Fields under Drought Condition – Seok-Won Jang et al, – Rice 

Integrated network modeling approach defines key metabolic responses of soil microbiomes to perturbations – Ryan S. McClure et al., – Scientific Reports 

Potential microbial bioindicators of phosphorus mining in a temperate deciduous forest – Laura M. Mason et al.,– Journal of Applied Microbiology

Phylogenetic signals and predictability in plant-soil feedbacks – Elizabeth M. Wandrag et al., – New Phytologist

Genomics / Bioinformatics

The compact genome of Giardia muris reveals important steps in the evolution of intestinal protozoan parasites – Feifei Xu et al., – Microbial Genomics 

LEMMI: A continuous benchmarking platform for metagenomics classifiers – Mathieu Seppey et al., – Genome Research

Other papers

Preprint: Metagenome-assembled genomes from Monte Cristo Cave (Diamantina, Brazil) reveal prokaryotic lineages as functional models for life on Mars – Amanda G Bendia et al., – BioRxiv 

Preprint: Exploring metal resistance genes and mechanisms in copper enriched metal ore metagenome – Esmaeil Forouzan Sr. et al., – BioRxiv

SARS-CoV-2 Preprints

Preprint: Alpha-1 antitrypsin inhibits SARS-CoV-2 infection – Lukas Wettstein et al., – BioRxiv

June 7, 2020

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Have a nice Sunday! Today, in this brief Digest, we have few papers about Microbiome and Health, including studies on Fibromyalgia, ALS and Hepatitis E infection. Additionally, we have papers about SARS-CoV-2. Stay safe!  

Microbiome research

Review: Microbiome in Health and Disease – Edward M Giles – Journal of Paediatrics and Child Health

Metabolic Syndrome, Depression, and Fibromyalgia Syndrome Prevalence in Patients With Irritable Bowel Syndrome: A Case-Control Study – Muharrem Bayrak – Medicine

Preprint: Large scale metagenome assembly reveals novel animal-associated microbial genomes, biosynthetic gene clusters, and other genetic diversity – Nicholas D Youngblut – bioRxiv

Amyotrophic Lateral Sclerosis and Intestinal Microbiota-Toward Establishing Cause and Effect – Marc Gotkine – Gut Microbes

Freeze-dried Fecal Samples Are Biologically Active After Long-Lasting Storage and Suited to Fecal Microbiota Transplantation in a Preclinical Murine Model of Clostridioides difficile Infection – Julie Reygner – Gut Microbes

Altered Fecal Microbiota on the Expression of Th Cells Responses in the Exacerbation of Patients With Hepatitis E Infection – Jian Wu – Journal of Viral Hepatitis

Covid-19 papers

Preprint: An OpenData portal to share COVID-19 drug repurposing data in real time – Kyle R. Brimacombe – bioRxiv

Preprint: Comparative study of four SARS-CoV-2 Nucleic Acid Amplification Test (NAAT) platforms demonstrates that ID NOW performance is impaired substantially by patient and specimen type – Paul Robert Lephart – bioRxiv

A Systematic Review of Neurological Manifestations of SARS-CoV-2 Infection: The Devil Is Hidden in the Details – Michele Romoli – European Journal of Neurology

Concomitant Brain Arterial and Venous Thrombosis in a COVID-19 Patient – Maria Malentacchi – European Journal of Neurology

February 28, 2020

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Good morning/afternoon y’all! today’s digest features some interesting-to-read genral biotech and ecology papers, as weel as the first gene catalouge of the vaginal microbiome, American pets microbiome revealed, cool microbiome engineering for biocontrol purpose in agriculture, a bunch of salt- and sweet-water microbiome studies and more!

Have a great weekend! put the guilt aside and enjoy some time with your spouse, family, pets, hobbies and anything else that you enjoy!

General Science

is is a very cool paper, beuatifuly presenting the connection and applicatino of two very ‘hot’ topics in today biotechnology world- AI and drug discovery:A Deep Learning Approach to Antibiotic Discovery- A Deep Learning Approach to Antibiotic Discovery, Jonathan M. Stokes, Cell

** Novel Outlook in Microbial Ecology: Nonmutualistic Interspecies Electron Transfer, Roman Moscoviz, Trends in Microbiology

A solution to minimum sample size for regressions, David J. Jenkins , PLOS One

The relationship between the host genome, microbiome, and host phenotype, Harald Brussow, Env. Micro.

Human microbiome

** A comprehensive non-redundant gene catalog reveals extensive within-community intraspecies diversity in the human vagina, Bing Ma, Nature Communications

Gut microbiota plasticity is correlated with sustained weight loss on a low-carb or low-fat dietary intervention, Jessica A. Grembi, Sci. Rep.

Analysis of healthy reference ranges for clinically relevant gut microbial indicators: A large web-based cohort study in Japan, Satoshi Watanabe , bioRxiv

Short chain fatty acids produced by colonizing intestinal commensal bacterial interaction with expressed breast milk are anti-inflammatory in human immature enterocytes, Nan Zheng, PLOS One

Animal microbiome

Characterization of gut microbiomes of household pets in the United States using a direct-to-consumer approach, Aashish R. Jha, PLOS One

Repeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome, Samuel J. Bowers, PLOS One

Insect microbiome

**Engineering bacterial symbionts of nematodes improves biocontrol potential of the western corn rootworm, Ricardo A. R. Machado, Nature Biotechnology

Plant and soil microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome, Siwen Deng , bioRxiv

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes, Yuting Liang , Env. Micro.

Network analysis infers the wilt pathogen invasion associated with non-detrimental bacteria, Qiolong Hu , npj biofims and microbiomes

Marine microbiome

Exploring the resistome, virulome and microbiome of drinking water in environmental and clinical settings, Marcela Franca Dias, Water Research

Niche partitioning of methane-oxidizing bacteria along the oxygen–methane counter gradient of stratified lakes, Magdalena J. Mayr, ISME

A metagenomic assessment of microbial eukaryotic diversity in the global ocean, Aleix Obiol, Mol. Eco. Res.

Ocean acidification affects microbial community and invertebrate settlement on biofilms, Katie S. Nelson, Sci. Rep.

Understanding and creating biocementing beachrocks via biostimulation of indigenous microbial communities, Asha A. Ramachandran , Env. Biotech.

February 8, 2020

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Have a nice Saturday, everyone! Today, in this Digest: several reviews, including some of them about the microbiome and Irritable Bowel Syndrome, Autism, Chemotherapy, C. difficile infection and more. Additionally, there is a very interesting study (Obata et al., Nature), showing new evidence about the relationship between the microbiota, the gut, and the nervous system. 

 

Human and General Microbiome

Neuronal programming by microbiota regulates intestinal physiology – Yuuki Obata – Nature

Fecal metatranscriptomics and glycomics suggest that bovine milk oligosaccharides are fully utilized by healthy adults – Samuel T. Westreich – The Journal of Nutritional Biochemistry

Review: Microbiome and Its Role in Irritable Bowel Syndrome – Mark Pimentel – Digestive Diseases and Sciences 

Review: Gut microbiota changes in children with autism spectrum disorder: a systematic review – Lucius Kang Hua Ho – Gut Pathogens

Review: Relationship Between the Gut Microbiome and Systemic Chemotherapy – Samantha M. Ervin – Digestive Diseases and Sciences 

Review: The infant gut microbiome as a microbial organ influencing host well-being – Francesca Turroni – Italian Journal of Pediatrics

Review: Increasing incidence of inflammatory bowel disease in children and adolescents: the significance of the environmental factors – Sowon Park – CEP

Review: Insights into the Role of Human Gut Microbiota in Clostridioides difficile Infection – Melina Kachrimanidou – Microorganisms (MDPI)

Review: Role of Dietary Nutrients in the Modulation of Gut Microbiota: A Narrative Review – Qi Yang – Nutrients

Opinion: Food, microbes, sex and old age: on the plasticity of gastrointestinal innervation – Tomotsune Ameku – Current Opinion in Neurobiology

The effects of proton pump inhibitors on the microbiome in young children – EI Levy – Acta Paedriatica

Targeted Approaches for In Situ Gut Microbiome Manipulation – Gail A. M. Cresci – JPEN

Dysbiosis of the Oral Ecosystem in Severe Congenital Neutropenia Patients – Egija Zaura – Proteomics Clinical Applications

Comparing Analytical Methods for the Gut Microbiome and Aging: Gut Microbial Communities and Body Weight in the Osteoporotic Fractures in Men (MrOS) Study – Michelle Shardell – The Journals of Gerontology: Series A

Oral and Gut Microbial Diversity and Immune Regulation in Patients with HIV on Antiretroviral Therapy – Medini K. Annavajhala – mSphere

Characteristics and Dysbiosis of the Gut Microbiome in Renal Transplant Recipients – J. Casper Swarte – Journal of Clinical Medicine

Comparison of serum microbiome composition in bipolar and major depressive disorders – Sang Jin Rhee – Journal of Psychiatric Research

 

Animal Microbiome / Animal Experiments

Review: Ruminal microbiome and microbial metabolome: effects of diet and ruminant host – C. J. Newbold – Animal

Review: Comparative methane production in mammalian herbivores – M. Clauss – Animal

Review: Regulation of gastrointestinal and renal transport of calcium and phosphorus in ruminants – M. R. Wilkens – Animal

Degeneration of the intestinal microbial community in PI3Kγ-knockout mice – Yi Li – Microbial Pathogenesis

Toxicity, gut microbiota and metabolome effects after copper exposure during early life in SD rats – Juan Dai – Toxicology

Evaluation of the effects of anthelmintic administration on the fecal microbiome of healthy dogs with and without subclinical Giardia spp. and Cryptosporidium canis infections – Madeline A. Fujishiro – PLoS ONE

Time of Feeding Alters Obesity-Associated Parameters and Gut Bacterial Communities, but Not Fungal Populations, in C57BL/6 Male Mice – Marie van der Merwe – CDN

Moderation effects of food intake on the relationship between urinary microbiota and urinary interleukin-8 in female type 2 diabetic patients – Fengping Liu – PeerJ

 

Beneficial Microbes and Compounds

Review: Surface components and metabolites of probiotics for regulation of intestinal epithelial barrier – Qing Liu – Microbial Cell Factories 

Polysaccharides from Polygonatum kingianum improve glucose and lipid metabolism in rats fed a high fat diet – Wen Gu – Biomedicine & Pharmacotherapy

Structural modulation of gut microbiota during alleviation of non-alcoholic fatty liver disease with Gynostemma pentaphyllum in rats – Shu-Hua Shen – BMC Complementary Medicine and Therapies

 

Plant Microbiome

Metagenomics methods for the study of plant-associated microbial communities: A review – Ayomide Emmanuel Fadiji – Journal of Microbiological Methods

Duckweed hosts a taxonomically similar bacterial assemblage as the terrestrial leaf microbiome – Kenneth Acosta – PLoS ONE

 

Bioinformatics

Computational Modeling of the Human Microbiome – Shomeek Chowdhury – Microorganisms (MDPI)

Unique k-mers as Strain-Specific Barcodes for Phylogenetic Analysis and Natural Microbiome Profiling – Valery V. Panyukov – International Journal of Molecular Sciences

February 2, 2020

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Have a nice Sunday! Today, in this Digest we have several papers about the relationship between the microbiome and different neurological/psychological conditions, such as ASD, depression or anxiety, or about the microbiome and the inflammatory bowel disease. Enjoy!

 

Human and General Microbiome

Review: Host-microbiota interactions in inflammatory bowel disease – Roberta Caruso – Nature Reviews Immunology 

Review: Considering gut microbiota in treatment of type 2 diabetes mellitus – Aneseh Adeshirlarijaney – Gut Microbes

Review: Gut Dysbiosis Dysregulates Central and Systemic Homeostasis via Suboptimal Mitochondrial Function: Assessment, Treatment and Classification Implications – George Anderson – Current Topics in Medicinal Chemistry

Book Chapter: Immune-Kynurenine Pathways and the Gut Microbiota-Brain Axis in Anxiety Disorders – Alper Evrensel – Anxiety Disorders 

Book Chapter: Autism and Gut-Brain Axis: Role of Probiotics – Saravana Babu Chidambaram – Personalized Food Intervention and Therapy for Autism Spectrum Disorder Management

Review: Microbial-Based and Microbial-Targeted Therapies for Inflammatory Bowel Diseases – Akihiko Oka – Digestive Diseases and Sciences

Precision Microbiome Modulation with Discrete Dietary Fiber Structures Directs Short-Chain Fatty Acid Production – Edward C. Deehan – Cell Host and Microbe

Urinary microbiome in uncomplicated and interstitial cystitis: is there any similarity? – Süleyman Yıldırım – World Journal of Urology

The gut microbiota response to helminth infection depends on host sex and genotype – Fei Ling – The ISME Journal 

Metabolism of multiple glycosaminoglycans by Bacteroides thetaiotaomicron is orchestrated by a versatile core genetic locus – Didier Ndeh – Nature Communications

Gestational diabetes and the human salivary microbiota: a longitudinal study during pregnancy and postpartum – Mie K. W. Crusell – BMC Pregnancy and Childbirth 

Vaginal dysbiosis associated-bacteria Megasphaera elsdenii and Prevotella timonensis induce immune activation via dendritic cells – Nienke H.van Teijlingen – Journal of Reproductive Immunology

Variability in Skin Microbiota between Smokers, Former Smokers, and Non-Smokers – Katherine G. Thompson – Journal of the American Academy of Dermatology

Microbiota changes and Intestinal Microbiota Transplantation in Liver Diseases and Cirrhosis – Jasmohan S. Bajaj – Journal of Hepatology

Host-Specific Evolutionary and Transmission Dynamics Shape the Functional Diversification of Staphylococcus epidermidis in Human Skin – Wei Zhou – Cell

 

Animal Microbiome and Animal Experiments

Effect of probiotic administration on gut microbiota and depressive behaviors in mice – Quan Feng Liu – DARU Journal of Pharmaceutical Sciences

Deciphering the bifidobacterial population within the canine and feline gut microbiota – Giulia Alessandri – Applied and Environmental Microbiology

Dissecting the factors shaping fish skin microbiomes in a heterogeneous inland water system – Yaron Krotman – Microbiome

Prenatal exposure to glufosinate ammonium disturbs gut microbiome and induces behavioral abnormalities in mice – Tianyu Dong – Journal of Hazardous Materials

High prevalence of Phasi Charoen-like virus from wild-caught Aedes aegypti in Grenada, W.I. as revealed by metagenomic analysis – Maria E. Ramos-Nino – PLoS ONE

Common structuring principles of the Drosophila melanogaster microbiome on a continental scale and between host and substrate – Yun Wang – Environmental Microbiology Reports

Community assembly of the native C. elegans microbiome is influenced by time, substrate, and individual bacterial taxa – Julia Johnke – Environmental Microbiology 

 

Environmental Microbiome

Patterns of local, intercontinental and inter-seasonal variation of soil bacterial and eukaryotic microbial communities – Johan De Gruyter – FEMS Microbiology Ecology

Dynamics and ecological distributions of the Archaea microbiome from inland saline lakes (Monegros Desert, Spain) – Mateu Menéndez-Serra – FEMS Microbiology Ecology

 

January 24, 2020

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Have a nice weekend! Today in this Digest, we have several papers about different interventions, microbes, and compounds with positive properties. And, of course, more papers. Enjoy.

 

Human and General Microbiome

Review: The microbiota and the hypothalamus-pituitary-adrenocortical (HPA) axis, implications for anxiety and stress disorders – Linoy Mia Frankiensztajn – Current Opinion in Neurobiology

Review: The Role of Meat Protein in Generation of Oxidative Stress and Pathophysiology of Metabolic Syndromes – Muhammad Ijaz Ahmad – Food Science of Animal Resources

Identifying determinants of bacterial fitness in a model of human gut microbial succession – Lihui Feng – PNAS

Reduced environmental bacterial load during early development and gut colonisation has detrimental health consequences in Japanese quail. – Ngare Wilkinson  – Heliyon

Review: Immunological Role of the Maternal Uterine Microbiome in Pregnancy: Pregnancies Pathologies and Alterated Microbiota – Jonah Bardos – Frontiers in Immunology

Association between the faecal short-chain fatty acid propionate and infant sleep – Anne-Louise M. Heath – European Journal of Clinical Nutrition

Prenatal dietary supplements influence the infant airway microbiota in a randomized factorial clinical trial – Mathis H. Hjelmsø – Nature Communications 

Physical fitness in community-dwelling older adults is linked to dietary intake, gut microbiota, and metabolomic signatures – Josué L. Castro‐Mejía – Aging Cell

Temporal Gut Microbial Changes Predict Recurrent Clostridiodes Difficile Infection in Patients With and Without Ulcerative Colitis – Allen A Lee – Inflammatory Bowel Diseases

Impacts of the Plateau Environment on the Gut Microbiota and Blood Clinical Indexes in Han and Tibetan Individuals – Zhilong Jia – mSystems

Intestinal microbes influence development of thymic lymphocytes in early life – Maria Ennamorati – PNAS

The cervicovaginal mucus barrier to HIV-1 is diminished in bacterial vaginosis – Thuy Hoang – PLoS Pathogens

Establishing high-accuracy biomarkers for colorectal cancer by comparing fecal microbiomes in patients with healthy families – Jian Yang – Beneficial Microbes

Characteristic gut microbiota and predicted metabolic functions in women with PCOS – Ling Zhou – Endocrine Connections 

Obese adolescents with PCOS have altered biodiversity and relative abundance in gastrointestinal microbiota – Beza Jobira – The Journal of Clinical Endocrinology & Metabolism

Association between blood omega-3 polyunsaturated fatty acids and the gut microbiota among breast cancer survivors – A. Horigome – Beneficial Microbes

Editorial: Processed food affects the gut microbiota: The revolution has started – Michael A Kamm – Journal of Gastroenterology and Hepatology

Commentary: mSphere of Influence: the Mycobiota in Human Health and Disease – Soo Chan Lee – mSphere

 

Animal Microbiota and Animal Model experiments

Letter: TCF-1 deficiency influences the composition of intestinal microbiota and enhances susceptibility to colonic inflammation – Guotao Yu – Protein & Cell 

Single-cell genomics of uncultured bacteria reveals dietary fiber responders in the mouse gut microbiota – Rieka Chijiiwa – Microbiome

Antidepressant treatment with fluoxetine during pregnancy and lactation modulates the gut microbiome and metabolome in a rat model relevant to depression – Anouschka S Ramsteijn – Gut Microbes

 

Beneficial Microbes and Compounds

Review: Fecal microbiota transplantation in disease therapy – Hanna Antushevich – Clinica Chimica Acta

Review: Microbiota and alcohol use disorder: are psychobiotics a novel therapeutic strategy? – Alicia Rodriguez-Gonzalez – Current Pharmaceutical Design

Mining possible associations of faecal A. muciniphila colonisation patterns with host adiposity and cardiometabolic markers in an adult population – E.K. Mitsou – Beneficial Microbes

Probiotics maintain intestinal secretory immunoglobulin A levels in healthy formula-fed infants: a randomised, double-blind, placebo-controlled study – L. Xiao – Beneficial Microbes

Effect of rice bran fermented with Saccharomyces cerevisiae and Lactobacillus plantarum on gut microbiome of mice fed high-sucrose diet – J. Shibayama – Beneficial Microbes

Inulin with different degrees of polymerization protects against diet-induced endotoxemia and inflammation in association with gut microbiota regulation in mice – Li-Li Li – Scientific Reports

Understanding the Scope of Do-It-Yourself Fecal Microbiota Transplant – Chiazotam Ekekezie – The American Journal of Gastroenterology

Milk Fermented by Lactobacillus paracasei NCC 2461 (ST11) Modulates the Immune Response and Microbiota to Exert its Protective Effects Against Salmonella typhimurium Infection in Mice – Leonardo Borges Acurcio – Probiotics and Antimicrobial Proteins 

Recovery of Lactobacillus casei strain Shirota (LcS) from faeces of healthy Singapore adults after intake of fermented milk – W.W.T. Khine – Beneficial Microbes

Seabuckthorn (Hippophaë rhamnoides) Freeze-Dried Powder Protects against High-Fat Diet-Induced Obesity, Lipid Metabolism Disorders by Modulating the Gut Microbiota of Mice – Caixia Guo – Nutrients

Chitooligosaccharides Modulate Glucose-Lipid Metabolism by Suppressing SMYD3 Pathways and Regulating Gut Microflora – Qiutong Wang – Marine Drugs

Lactobacillus and Pediococcus ameliorate progression of non-alcoholic fatty liver disease through modulation of the gut microbiome – Na Young Lee – Gut Microbes

Review: Antimicrobials for food and feed; a bacteriocin perspective – Paula M O’Connor – Current Opinion in Biotechnology

 

Bioinformatics

Transfer index, NetUniFrac and some useful shortest path-based distances for community analysis in sequence similarity networks – Henry Xing – Bioinformatics

MICOM: Metagenome-Scale Modeling To Infer Metabolic Interactions in the Gut Microbiota – Christian Diener – mSystems