October 24, 2020

Greetings from Santiago, Chile! Today, in this Digest we have several reviews about microbiota and different conditions or interventions. We have also papers about the microbial evolution and its relationship with the host, the role of O-glycosylated mucus, the microbiome of neonates and the influence of probiotics, and more…    

Human and General Microbiome

Review: The gut microbiota-brain axis in behaviour and brain disorders – Livia H. Morais – Nature Reviews Microbiology

Review: Gut microbiota in pancreatic diseases: possible new therapeutic strategies – Li-long Pan – Acta Pharmacologica Sinica 

Review: The Gut Microbiome and the Triple Environmental Hit Concept of Inflammatory Bowel Disease Pathogenesis – Richard Kellermayer – Journal of Pediatric Gastroenterology and Nutrition

Review: Allogenic stem cell transplant-associated acute graft versus host disease: a computational drug discovery text mining approach using oral and gut microbiome signatures – M. F. Beckman – Supportive Care in Cancer 

Experimental evolution makes microbes more cooperative with their local host genotype – Rebecca T. Batstone – Science

Proximal colon-derived O-glycosylated mucus encapsulates and modulates the microbiota – Kirk Bergstrom – Science

The Microbiota Profile in Inflamed and Non-Inflamed Ileal Pouch-Anal Anastomosis – Sabrina Just Kousgaard – Microorganisms (MDPI)

Altered Gut Microbiome and Environmental Factors Associated with Development of Eczema in Hong Kong Infants: A 4-Month Pilot Study – Carmen Wing Han Chan – International Journal of Environmental Research and Public Health

Beneficial microbes and Compounds

Systematic Review: The role of pro-, pre- and symbiotics in cancer: A systematic review – Miarons Marta – Journal of Clinical Pharmacy and Therapeutics

Review: Fiber and Prebiotic Interventions in Pediatric Inflammatory Bowel Disease: What Role Does the Gut Microbiome Play? – Genelle R. Healey – Nutrients (MDPI)

Influence of probiotic supplementation on the developing microbiota in human preterm neonates – Niels van Best – Gut Microbes

Anti-Inflammatory and Intestinal Microbiota Modulation Properties of Jinxiang Garlic ( Allium sativum L.) Polysaccharides toward Dextran Sodium Sulfate-Induced Colitis – Xin Shao – Journal of Agricultural and Food Chemistry

Food Microbiome

Metagenomic characterization of bacterial community and antibiotic resistance genes in representative ready-to-eat food in southern China – YiMing Li – Scientific Reports

Animal Microbiome

Review: Toxin Degradation by Rumen Microorganisms: A Review – Zhi Hung Loh – Toxins (MDPI)

Gut dysbiosis associated with the rats’ responses in methamphetamine-induced conditioned place preference – Cheng Yang – Addiction Biology

A High-Fat Diet Increases Gut Microbiota Biodiversity and Energy Expenditure Due to Nutrient Difference – Botao Wang – Nutrients (MDPI)

Plant Microbiome

Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava – Lin Zhang – Plant Biotechnology Journal

Daring to be differential: metabarcoding analysis of soil and plant-related microbial communities using amplicon sequence variants and operational taxonomical units – Lisa Joos – BMC Genomics


Clustering on Human Microbiome Sequencing Data: A Distance-Based Unsupervised Learning Model – Dongyang Yang – Microorganisms (MDPI)

A generalized machine-learning aided method for targeted identification of industrial enzymes from metagenome: a xylanase temperature dependence case study – Mehdi Foroozandeh Shahraki – Biotechnology and Bioengeenering

October 17, 2020

Have a nice weekend! Today, in this brief Digest, several papers about microbiome studies in animal models. Additionally, some highlighted studies in humans: the vaginal microbiota in a Swedish cohort, and the microbiota from the urinary tract, by the use of culturomics.

Human and General Microbiome

Using data science for medical decision making case: role of gut microbiome in multiple sclerosis – Jasminka Hasic Telalovic- BMC Medical Informatics and Decision Making

Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut – Grégory Dubourg – Frontiers in Microbiology

Vaginal microbiota and human papillomavirus infection among young Swedish women – Liqin Cheng – npj Biofilms and Microbiomes

Review: Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities – Saad Khan – Annual Review of Pharmacology and Toxicology 

Animal Microbiome

Developmental stages in microbiota, bile acids, and clostridial species in healthy puppies – Amanda B. Blake – Journal of Veterinary Internal Medicine

Screening of Microbes Associated With Swine Growth and Fat Deposition Traits Across the Intestinal Tract – Shi Tang – Frontiers in Microbiology

Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats – Qinghong Li – Frontiers in Microbiology

Inulin alleviates adverse metabolic syndrome and regulates intestinal microbiota composition in Nile Tilapia ( Oreochromis niloticus) fed with high-carbohydrate diet – Tong Wang – British Journal of Nutrition

Minireview: Transmission of the sponge microbiome: moving towards a unified model – Bruno Francesco Rodrigues de Oliveira  – Environmental Microbiology Reports 

Co-selection of antibiotic resistance genes, and mobile genetic elements in the presence of heavy metals in poultry farm environments – Sohaib H.Mazhar – Science of The Total Environment

Friend or foe? Effects of host immune activation on the gut microbiome in the caterpillar Manduca sexta – Laura E. McMillan – Journal of Experimental Biology

Environmental Microbiome

Correspondence: Towards meaningful scales in ecosystem microbiome research – Francisco Dini‐Andreote – Environmental Microbiology

Preprint: Genomics-accelerated discovery of diverse fungicidal bacteria – Matthew B Biggs – BioXriv

Preprint: Functional repertoire convergence of distantly related eukaryotic plankton lineages revealed by genome-resolved metagenomics – Tom O. Delmont – BioXriv

Beneficial Microbes and Compounds

The chemopreventive effects of Huangqin-tea against AOM-induced preneoplastic colonic aberrant crypt foci in rats and omics analysis – Jie Shen – Food & Function

Prophylactic effects of oral administration of Lactobacillus casei on house dust mite-induced asthma in mice – Lingzhi Li – Food & Function

Lactobacillus plantarum Shinshu N-07 isolated from fermented Brassica rapa L. attenuates visceral fat accumulation induced by high-fat diet in mice – T. Yin – Beneficial Microbes

September 19, 2020

Have a nice weekend! Today, in this digest: a pair of papers released in Science, showing interesting results about the dialogue between the microbiota and the host. In Mager et al., the study showed that inosine, a metabolite released by microbes, may have an adjuvant role in cancer immune treatment. In the Lobel et al. paper, they demostrated that “diet can tune microbiota function to support healthy host physiology through posttranslational modification without altering microbial community composition”.

And of course, there are more papers 🙂 

Human and General Microbiome

Microbiome-derived inosine modulates response to checkpoint inhibitor immunotherapy – Lukas F. Mager – Science

> Perspective about this paper: Messengers from the microbiota – Fyza Y. Shaikh 

Diet posttranslationally modifies the mouse gut microbial proteome to modulate renal function – Lior Lobel – Science 

>  Perspective about this paper: The gut microbiota in kidney disease – Jennifer L. Pluznick

Fecal microbiota transplantation in inflammatory bowel disease patients: A systematic review and meta-analysis – Luciane de Fátima Caldeira – Plos One

Minireview: Antimicrobial peptides in the gut-brain axis: A straightforward review to unravel some missing links – Fabiano Pinheiro da Silva – Journal of Neuroscience Research

Microbiome analysis of contact lens care solutions and tear fluids of contact lens wearers: Possible involvement of streptococcal antigens in allergic symptoms related to contact lens wear – Fumika Hotta – International Journal of Molecular Medicine

Longitudinal Changes in Skin Microbiome and Microbes Associated with Change in Skin Status in Patients with Psoriasis – Hailun Wang – Acta Dermato Venereologica

Changes in fecal short-chain fatty acids following fecal microbiota transplantation in patients with irritable bowel syndrome – Magdy El‐Salhy – Neurogastroenterology and Motility

Analysis of airway microbiota in adults from a Brazilian cystic fibrosis center – Cassiana Costa Ferreira Leite – Brazilian Journal of Microbiology

Bacterial diversity and inflammatory response at first-time visit in younger and older individuals with diabetic foot infection (DFI) – Stefan Dörr – Acta Diabetologica 

Animal Microbiome

Harnessing the strategy of metagenomics for exploring the intestinal microecology of sable (Martes zibellina), the national first-level protected animal – Jiakuo Yan – AMB Express

The Gut Microbial Community Structure of the North American River Otter (Lontra canadensis) in the Alberta Oil Sands Region in Canada: Relationship with Local Environmental Variables and Metal Body Burden – Galen Guo – Environmental Toxicology and Chemistry

Dynamic changes of the fecal bacterial community in dairy cows during early lactation – Shuai Huang – AMB Express

Comparative analysis of the pulmonary microbiome in healthy and diseased pigs – Zongjie Li – Molecular Genetics and Genomics

Plant microbiome

Functional gene categories differentiate maize leaf drought-related microbial epiphytic communities – Barbara A. Methe – Plos One

Microbiome and diet

Minireview: Soy bioactive peptides and the gut microbiota modulation – Tolulope Joshua Ashaolu – Applied Microbiology and Biotechnology 

September 16, 2020

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


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

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 TreatmentCancers (MDPI)

Review: Influence of Resveratrol on the Cardiovascular Health Effects of Chronic Kidney DiseaseInternational 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


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

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

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

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 homeostasisChuanhai 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

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 8, 2020

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



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