September 20, 2018

Today’s digest presents reviews covering potential of microbiome in olfactory communication and oral-gut microbiome axis in rheumatoid arthritis; articles on association of human gut microbiome with different diseases; news on antibiotics and scientific data on personality types in humans.

General microbiome

Review: The Extended Genotype: Microbially Mediated Olfactory Communication – Alexandra J.R. Carthey – Trends in Ecology and Evolution

Talk to your gut: the oral-gut microbiome axis and its immunomodulatory role in the etiology of rheumatoid arthritis – Marines du Teil Espina – FEMS Microbiology Reviews

Commmentary: Regulating stool for microbiota transplantation – Pilar N Ossorio – Gut microbes

Proteomics and the microbiome: pitfalls and potential – Huafeng Lin – Expert Review of Proteomics

Pregnancy and early life

Postnatal exposure to household disinfectants, infant gut microbiota and subsequent risk of overweight in children – Mon H. Tun – Canadian Medical Association Journal

Human gut microbiome

Gut Microbiota Differs in Composition and Functionality Between Children With Type 1 Diabetes, MODY2, and Healthy Control Subjects: A Case-Control Study – Isabel Leiva-Gea – Diabetes Care

Analysis of gut microbiota profiles and microbe-disease associations in children with autism spectrum disorders in China – Mengxiang Zhang – Scientific Reports

Mucosal microbiota of intestinal polyps reveals putative biomarkers of colorectal cancer – Marta Mangifesta – Scientific Reports

Predicting recurrence of Clostridium difficile infection following encapsulated fecal microbiota transplantation – Christopher Staley – Microbiome

Could fecal phenylacetic and phenylpropionic acids be used as indicators of health status? – Isabel Gutiérrez-Díaz – Journal of Agricultural and Food Chemisty

Altered intestinal antibacterial gene expression response profile in irritable bowel syndrome is linked to bacterial composition and immune activation – Sean M. P. Bennet – Neurogastroenterology and Motility

Animal experiments

Melatonin reprogramming of gut microbiota improves lipid dysmetabolism in high fat diet-fed mice – Jie Yin – Journal of Pineal Research

Water and extremophile microbiome

Dynamics of microbial populations mediating biogeochemical cycling in a freshwater lake – Keith Arora-Williams – Microbiome

Probiotics/Prebiotics

The Impact of Probiotic Supplements on Cognitive Parameters in Euthymic Individuals with Bipolar Disorder: A Pilot Study – Eva Z Reininghaus – Neuropsychobiology

Microbes in the news

The case for expensive antibioticshttp://www.wired.com

Crucial antibiotics still used on US farms despite public health fear  The Guardian

Non-microbiology picks

A robust data-driven approach identifies four personality types across four large data sets – Martin Gerlach – Nature Human Behaviour

 

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August 30, 2018

Today’s digest covers population based studies on regional specificity of the gut microbiome, guidelines on use of fecal microbiota transplant, and review articles on role of the gut microbiome in colorectal cancer, liver tumors and functional gastrointestinal disorders. Also includes articles on how xenobiotics and psychotropic drugs affect the gut microbiota, and link to wonderful bacterial art!

General microbiome

Regional variation limits applications of healthy gut microbiome reference ranges and disease models – Yan He – Nature Medicine

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography – Melanie Deschasaux – Nature Medicine

The use of faecal microbiota transplant as treatment for recurrent or refractory Clostridium difficile infection and other potential indications: joint British Society of Gastroenterology (BSG) and Healthcare Infection Society (HIS) guidelines – Benjamin H Mullish – Gut

Bile Acids, the Microbiome, Immunity, and Liver Tumors – Christoph Schramm – The New England Journal of Medicine

Review: The gut microbiome and colorectal cancer: a review of bacterial pathogenesis – Jessica D. Dahmus – Journal of Gastrointestinal Oncology

Human gut microbiome

Review: The Gut Microbiome in Adult and Pediatric Functional Gastrointestinal Disorders – Andrea Shin – Clinical Gastroenterology and Hepatology

Changes in microbiota composition, bile and fatty acid metabolism, in successful faecal microbiota transplantation for Clostridioides difficile infection – Jillian RM Brown – BMC Gastroenterology

“Cocktail” of Xenobiotics at Human Relevant Levels Reshapes the Gut Bacterial Metabolome in a Species-Specific Manner – Yingdan Zhang – Environmental Science and Technology

Animal experiments

Microbial Sensing by Intestinal Myeloid Cells Controls Carcinogenesis and Epithelial Differentiation – Naoteru Miyata – Cell Reports

Transplacental immune modulation with a bacterial-derived agent protects against allergic airway inflammation – Kyle T Mincham – Journal of Clinical Investigation

Differential effects of psychotropic drugs on microbiome composition and gastrointestinal function – Sofia Cussotto – Pschycopharmocology

Butyrate and Dietary Soluble Fiber Improve Neuroinflammation Associated With Aging in Mice – Stephanie M Matt – Frontiers in Immunonology

Correlations between intestinal innate immune genes and cecal microbiota highlight potential for probiotic development for immune modulation in poultry – Nicky-Lee Willson – Applied Microbiology and Biotechnology

Plant, root, and soil microbiome

Convergence between the microcosms of Southeast Asian and North American pitcher plants – Leonora S Bittleston – Elife

Water and extremophile microbiome 

In situ development of a methanotrophic microbiome in deep-sea sediments – S E Ruff – ISME Journal

Probiotics/Prebiotics

Probiotics for management of infantile colic: a systematic review of randomized controlled trials – Radoslaw Dryl – Archives of Medical Science

Bioinformatics

A multi-source domain annotation pipeline for quantitative metagenomic and metatranscriptomic functional profiling – Ari Ugarte – Microbiome

Microbes in the news

The world’s smallest masterpieces? Microscopic version of Leonardo da Vinci’s Mona Lisa and portraits of Albert Einstein and Charles Darwin are recreated using MILLIONS of bacteria – Daily Mail

Non-microbiology picks 

Evaluating the replicability of social science experiments in Nature and Science between 2010 and 2015 – Colin F Camerer – Nature Human Behaviour

 

August 22, 2018

Today’s digest is a mix of exciting reviews and research articles. The research articles are about – association between (site-specific) microbiota changes and stunded chilhood growth, bronchopulmonary dysplasia and Ankylosing Spondylitis; new tools to analyze mother-infant phage transmission; and low cost platform to analyze gut microbiota and host biomarkers. Also includes statement from FDA on regulation of live microbiome-based products, and comparison of single versus multiple strain probiotics in intestinal dysbiosis.

General microbiome

Review: Microbiology of the built environment – Jack A Gilbert – Nature Reviews Microbiology

Considerations for Best Practices in Studies of Fiber or Other Dietary Components and the Intestinal Microbiome – David M Klurfeld – American Journal of Physiology Endocrinology and Metabolism

Review: Impact of the commensal microbiota in atherosclerosis and arterial thrombosis – Klytaimnistra Kiouptsi – British Journal of Pharmacology

Pregnancy and early life

Metagenomic analysis with strain-level resolution reveals fine-scale variation in the human pregnancy microbiome – Daniela SA Goltsman – bioRxiv

Human respiratory microbiome

Early Airway Microbial Metagenomic and Metabolomic Signatures are Associated with Development of Severe Bronchopulmonary Dysplasia – Charitharth V Lal – American Journal of Physiology

Human gut microbiome

Stunted childhood growth is associated with decompartmentalization of the gastrointestinal tract and overgrowth of oropharyngeal taxa – Pascale Vonaesch – PNAS

Tracing mother-infant transmission of bacteriophages by means of a novel analytical tool for shotgun metagenomic datasets: METAnnotatorX – Christian Milani – Microbiome

Altered Bacteria-Fungi Inter-Kingdom Network in Gut of Ankylosing Spondylitis Patients – Ming Li – bioRxiv

Animal experiments

Hyperactivated PI3Kd promotes self and commensal reactivity at the expense of optimal humoral immunity – Silvia Preite – Nature Immunology

The Potential Role of the Dipeptidyl Peptidase-4-Like Activity From the Gut Microbiota on the Host Health – Marta Olivares – Frontiers in Microbiology

Plant, root, and soil microbiome

Effects of compost containing oxytetracycline on enzyme activities and microbial communities in maize rhizosphere soil – Lisha Zhen – Environmental Science and Pollution Research

Impact of soil salinity on the microbial structure of halophyte rhizosphere microbiome – Salma Mukhtar – World Journal of Microbiology and Biotechnology

Water and extremophile microbiome

Inter-Kingdom beach warfare: Microbial chemical communication activates natural chemical defences – Zeinab G Khalil – The ISME Journal

Biogeography and taxonomic overview of terrestrial hot spring thermophilic phages – Olivier Zablocki – Extremophiles

Food microbiology

How Fine Structural Differences of Xylooligosaccharides and Arabinoxylooligosaccharides Regulate Differential Growth of Bacteroides Species – Mihiri Mendis – Journal of Agricultural and Food Chemistry

Probiotics / prebiotics

Influence of monostrain and multistrain probiotics on immunity, intestinal ultrastructure and microbiota in experimental dysbiosis – E Ermolenko – Beneficial Microbes

Effect of probiotic Bifidobacterium bifidum G9-1 on the relationship between gut microbiota profile and stress sensitivity in maternally separated rats – Hirokazu Fukui – Scientific Reports

Techniques

A low-cost paper-based synthetic biology platform for analyzing gut microbiota and host biomarkers – Melissa K Takahashi – Nature Communications

Microbes in the news

Statement from FDA Commissioner Scott Gottlieb, M.D., on advancing the science and regulation of live microbiome-based products used to prevent, treat, or cure diseases in humans – Food and Drug Administration

Non-microbiology picks

Mechanisms regulating intestinal barrier integrity and its pathological implications – Chaithanya Chelakkot – Experimental and Molecular Medicine

 

Article post

Microbiota depletion shifts colonocyte substrate utilization

In the fed state, glucose is the major fuel to most cell types in the body. In contrast, colonic epithelial cells or colonocytes utilize butyrate as their major energy source. Butyrate is one of the short chain fatty acids (SCFAs), a class of microbial metabolites produced by microbial fermentation of dietary fiber in gut. When the gut microbiota is depleted, such as in germ-free (GF) mice, butyrate levels along with other SCFAs decline prompting “starved” colonocytes to shift their substrate utilization to an alternative fuel, such as glucose.

Glucose undergo oxidative metabolism in cells to produce energy. In contrast, early ex vivo experiments studying substrate utilization in isolated colonocytes of rats using radioactive tracers revealed that about 80% of glucose is rather converted into lactate in colonocytes [1]. Later Donohoe et al., found that colonocytes from GF mice produce approx. 4 times higher lactate compared with conventionally raised mice through anaerobic glycolysis of glucose [2]. However, lactate production is not an energy rewarding process and yields only 2-4 ATP compared with 36 ATPs from oxidative phosphorylation of glucose. Thus, the authors concluded that despite the shift in substrate utilization, the colonocytes in the GF mice remain in energy insufficient state [2].

In the recent article published in Nature Communications by Zarrinpar et al. [3], where gut microbiota (and butyrate!) was depleted using multiple gavage of antibiotics over the course of 4 weeks. The authors found that cecum tissue uses glucose as an alternative fuel in the absence of butyrate, and that the expression levels of 8 out of 10 enzymes in glycolysis pathway were upregulated in cecum of antibiotic- compared with vehicle-treated mice. Finally, they speculate that due to shift in substrate utilization in cecum, gut becomes a glucose sink that could account for overall improvement in glucose metabolism in the antibiotic-treated mice [3].

Perhaps this speculation needs more careful investigation. It is true that colonocytes use butyrate as their primary fuel; however, butyrate is not synthesized in isolation. Gut microbiota produces SCFAs that include acetate, propionate and butyrate. It has been shown that colonocytes prefer other SCFA such as acetate over glucose [4] probably because anaerobic glycolysis of glucose does not yield enough energy. In the article by Zarrinpar et al., there was a trend towards reduction of acetate in antibiotic- compared with vehicle-treated mice, but it was not depleted to the same level as butyrate [3]. Secondly, shift in colonocyte substrate utilization from butyrate to glucose is also observed in inflammatory bowel disease and DSS colitis model. This is indicated to be due to alteration in butyrate uptake and thus colonocytes utilize glucose leading to high amount of lactate accumulation in cells [5]. However, patients with IBS are more prone to develop glucose intolerance than the healthy people.

Studying substrate utilization in cecum/colonocytes is complex. It is true that the isolated colonocytes do not reflect the in vivo scenario. However, transcriptomic data (showing increased expression of glycolytic enzymes in intestinal tissue of antibiotic-treated mice) probably needs to be backed with enzyme activity measurements and tracer studies to  understand its impact on overall metabolism.

1. Ardawi, M.S. and E.A. Newsholme, Fuel utilization in colonocytes of the rat. Biochem J, 1985. 231(3): p. 713-9.

2. Donohoe, D.R., et al., Microbial regulation of glucose metabolism and cell-cycle progression in mammalian colonocytes. PLoS One, 2012. 7(9): p. e46589.

3. Zarrinpar, A., et al., Antibiotic-induced microbiome depletion alters metabolic homeostasis by affecting gut signaling and colonic metabolism. Nat Commun, 2018. 9(1): p. 2872.

4. Clausen, M.R. and P.B. Mortensen, Kinetic studies on the metabolism of short-chain fatty acids and glucose by isolated rat colonocytes. Gastroenterology, 1994. 106(2): p. 423-32.

5. Thibault, R., et al., Butyrate utilization by the colonic mucosa in inflammatory bowel diseases: a transport deficiency. Inflamm Bowel Dis, 2010. 16(4): p. 684-95.

July 25, 2018

Today’s digest consists of opinion paper from European MyNewGut project, review article on gut microbiota dysbiosis, and meta-analysis to find association between antibiotic associated microbiota perturbation and childhood obesity. Also includes application of contraceptive rings and probiotic capsules to increase vaginal lactobacilli, and how preprint publishing could create confusion in public journalism!

General microbiome

Towards microbiome-informed dietary recommendations for promoting metabolic and mental health: Opinion papers of the MyNewGut project – Yolanda Sanz – Clinical Nutrition

Review: The gut microbiota: A new target in the management of alcohol dependence? – Sophie Leclercq – Alcohol

Review: Low diversity gut microbiota dysbiosis: drivers, functional implications and recovery – Michael Kriss – Current Opinion in Microbiology

Review: Environmental factors, gut microbiota, and colorectal cancer prevention – Mingyang Song – Clinical Gastroenterology and Hepatology

Review: The association between antibiotic use in infancy and childhood overweight or obesity: a systematic review and meta-analysis – SA Miller – Obesity Reviews

Multi-site human microbiome

Unique subgingival microbiota associated with periodontitis in cirrhosis patients – Anders Jensen – Scientific Reports

Human respiratory microbiome

A Metagenomic Comparison of Tracheal Aspirate and Mini-Bronchial Alveolar Lavage for Assessment of Respiratory Microbiota – Katrina Kalantar – bioRxiv

Human vaginal microbiome

Contraceptive rings promote vaginal lactobacilli in a high bacterial vaginosis prevalence population: A randomised, open-label longitudinal study in Rwandan women – Tania Crucitti – PlosOne

Comparative phase I randomized open-label pilot clinical trial of Gynophilus® (Lcr regenerans®) immediate release capsules versus slow release muco-adhesive tablets – Caroline Dausset – European Journal of Clinical Microbiology and Infectious Diseases

Human gut microbiome

Association Between Intestinal Microbiota Collected at Hospital Admission and Outcomes of Patients with Cirrhosis – Jasmohan S Bajaj – Clinical Gastroenterology and Hepatology

Animal experiments

Butyrate regulates inflammatory cytokine expression without affecting oxidative respiration in primary astrocytes from spontaneously hypertensive rats – Tao Yang – Physiological Reports

Plant, root, and soil microbiome

Quantitative stable isotope probing with H218O reveals that most bacterial taxa in soil synthesize new ribosomal RNA – Katerina Papp – The ISME Journal

Community structure and plant growth-promoting potential of cultivable bacteria isolated from Cameroon soil – Gylaine VT Tchakounte – Microbiological Research

Water and extremophile microbiome

Effects of mercury addition on microbial community composition and nitrate removal inside permeable reactive barriers – Kenly Hiller-Bittrolff – Environmental Pollution

Food microbiology

Food Chemicals Disrupt Human Gut Microbiota Activity And Impact Intestinal Homeostasis As Revealed By In Vitro Systems – Clemence Defois – Scientific Reports

Polyol-producing lactic acid bacteria isolated from sourdough and their application to reduce sugar in a quinoa-based milk substitute – Stephanie Jeske – International Journal of Food Microbiology

Probiotics / prebiotics

Probiotics in cystic fibrosis patients: A double blind crossover placebo controlled study: Pilot study from the ESPGHAN Working Group on Pancreas/CF – Stephanie Van Biervliet – Clinical Nutrition ESPEN

Phages and viruses

Parvovirus Minute Virus of Mice Interacts with Sites of Cellular DNA Damage to Establish and Amplify its Lytic Infection – Kinjal Majumder – eLife

Techniques

Review: The evolving interface between synthetic biology and functional metagenomics – Eric Van der Helm – Nature Chemical Biology

Targeted analysis of microbial-generated phenolic acid metabolites derived from grape flavanols by gas chromatography-triple quadrupole mass spectrometry – Eileen Carry – Journal of Pharmaceutical and Biomedical Analysis

Science, publishing, and career 

Preprints could promote confusion and distortion – Nature News

Science-adjacent’ conferences and why they matter – Nature News

Tulika’s non-microbiology picks

Metformin inhibits gluconeogenesis via a redox-dependent mechanism in vivo – Anila K Madiraju – Nature Medicine

 

July 04, 2018

Today’s Digest is about association of the microbiome at various mucosal sites with different diseases in humans, germ-free chicken and microbial community in anoxic inter-tidal zone of Earth to study Lacustrine system of Mars. You can also read about BacStalk- software to analyze bacterial images, Chinese baby project and how air pollution is contributing to incidence of diabetes.

General microbiome

Review: Gut associated bacteria are critical to metabolism, inflammation and health – Philip Newsholme – Current Opinion in Clinical Nutrition and Metabolic Care

Review: The Microbiome and Acute Kidney Injury – H Rabb – Nephron

Multi-site human microbiome

Review: Cariogenic microbiome and microbiota of the early primary dentition: a contemporary overview – Kausar Sadia Fakhruddin – Oral Diseases

Dysbiosis of oral microbiota and its association with salivary immunological biomarkers in autoimmune liver disease – Kazumichi Abe – PlosOne

Human respiratory microbiome

Severe Obstructive Sleep Apnea is Associated with Alterations in the Nasal Microbiome and Increase in Inflammation – Benjamin G Wu – American Journal of Respiratory and Critical Care Medicine

Microbiota Composition and the Integration of Exogenous and Endogenous Signals in Reactive Nasal Inflammation – Francesco Antonio Salzano – Journal of Immunology Research

Human skin microbiome

Inflammatory cytokines and biofilm production sustain Staphylococcus aureus outgrowth and persistence: a pivotal interplay in the pathogenesis of Atopic Dermatitis – E.G.Di Domenico – Scientific reports

Human vaginal microbiome

Complex ecological interactions of Staphylococcus aureus in tampons during menstruation – Isaline Jacquemond – Scientific Reports

Human gut microbiome

Altered Intestinal Microbiota with Increased Abundance of Prevotella Is Associated with High Risk of Diarrhea-Predominant Irritable Bowel Syndrome – Tingting Su – Gastroenterology Research and Practice

The presence of genetic risk variants within PTPN2 and PTPN22 is associated with intestinal microbiota alterations in Swiss IBD cohort patients – Bahtiyar Yilmaz – PlosOne

Animal experiments 

Gut Microbial succession during conventionalization of germfree chicken – Thomas Milton – bioRxiv

Early-life antibiotics attenuate regulatory T cell generation and increase the severity of murine house dust mite-induced asthma – Alexander J. Adami – Pediatric Research

Changes in intestinal gene expression and microbiota composition during late pregnancy are mouse strain dependent – Marlies Elderman – Scientific Reports

Critical Roles for Microbiota-Mediated Regulation of the Immune System in a Prenatal Immune Activation Model of Autism – Catherine R. Lammert – The Journal of Immunology

Plant, root, and soil microbiome

Cascading effects of elevated ozone on wheat rhizosphere microbial communities depend on temperature and cultivar sensitivity – F. Changey – Environmental Pollution

Litter quality drives the differentiation of microbial communities in the litter horizon across an alpine treeline ecotone in the eastern Tibetan Plateau – Haifeng Zheng – Scientific Reports

Identification of a Novel Feruloyl Esterase by Functional Screening of a Soil Metagenomic Library – Xuanxuan Li – Applied Biochemistry and Biotechnology

Water and extremophile microbiome

Quorum sensing and iron regulate a two-for-one siderophore gene cluster in Vibrio harveyi – Darcy L. McRose – PNAS

Identifying labile DOM components in a coastal ocean through depleted bacterial transcripts and chemical signals – Alexey Vorobev – Environmental Microbiology

Metabolic potential of microbial communities from ferruginous sediments – Aurele Vuillemin – Environmental Microbiology

Microbes in space

The Microbial Community of a Terrestrial Anoxic Inter-Tidal Zone: A Model for Laboratory-Based Studies of Potentially Habitable Ancient Lacustrine Systems on Mars – Elliot Curtis-Harper – Microorganisms

Phages and viruses

Development of a high-throughput assay to detect antibody inhibition of low pH induced conformational changes of influenza virus hemagglutinin – Jessica F. Trost – PlosOne

Techniques

Review: Errors during Gene Expression: Single-Cell Heterogeneity, Stress Resistance, and Microbe-Host Interactions – Christpher R. Evans – mBio

BacStalk: a comprehensive and interactive image analysis software tool for bacterial cell biology – Raimo Hartmann – bioRxiv

Assessing the Mouse Intestinal Microbiota in Settings of Type-2 Immune Responses – Mei San Tang – Type 2 Immunity

Microbes in the news

Bacteria can ‘divide and conquer’ to vanquish their enemies – Science Daily

Gigantic study of Chinese babies yields slew of health data – Nature News

Non-microbiology picks

The 2016 global and national burden of diabetes mellitus attributable to PM2·5 air pollution – Benjamin Bowe – The Lancet Planetary Health