Metsky HC, Siddle KJ, Gladden-Young A, Qu J, Yang DK, Brehio P, Goldfarb A, Piantadosi A, Wohl S, Carter A, Lin AE, Barnes KG, Tully DC, Corleis B, Hennigan S, Barbosa-Lima G, Vieira YR, Paul LM, Tan AL, Garcia KF, Parham LA, Odia I, Eromon P, Folarin OA, Goba A, Simon-Lorière E, Hensley L, Balmaseda A, Harris E, Kwon DS, Allen TM, Runstadler JA, Smole S, Bozza FA, Souza TML, Isern S, Michael SF, Lorenzana I, Gehrke L, Bosch I, Ebel G, Grant DS, Happi CT, Park DJ, Gnirke A, Sabeti PC, Matranga CB. Nat Biotechnol. 02 2019. doi: 10.1038/s41587-018-0006-x.
COMMENT: Sequencing of patient samples for detection and characterization of human viral pathogens is hampered by the low viral titers or high levels of host material. New tools are needed that improve metagenomic sequencing sensitivity. Previous... + info
Chan S, Pullerits K, Keucken A, Persson KM, Paul CJ, Rådström P. NPJ Biofilms Microbiomes. 2019. doi: 10.1038/s41522-019-0082-9.
COMMENT: Drinking water is delivered through pipes of drinking water distribution systems (DWDSs), these pipes are lined with biofilm that could affect water quality by releasing bacteria into the drinking water. This study describes the drinking... + info
Composition and Variation of the Human Milk Microbiota Are Influenced by Maternal and Early-Life Factors.
Moossavi S, Sepehri S, Robertson B, Bode L, Goruk S, Field CJ, Lix LM, de Souza RJ, et al.. Cell Host Microbe. 2019 Feb 13;25(2):324-335.e4.
COMMENT: The breastmilk contains a complex community of bacteria but the determinants of milk microbiota are mostly unknown. This study uses multiple analytic approaches to analyze the human milk microbiota in a large population cohort and provides... + info
Allemann A, Kraemer JG, Korten I, Ramsey K, Casaulta C, Wüthrich D, Ramette A, Endimiani A, Latzin P, Hilty M. Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00212.
COMMENT: It has been reported that patients with cystic fibrosis (CF) have complex lung microbiota with many genetic exchanges occurring by horizontal gene transfer, promoting the emergence of multidrug-resistant bacteria. This study analyzed the... + info
Verkhnyatskaya S, Ferrari M, de Vos P, Walvoort MTC. Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00343.
COMMENT: Many factors have impact on the composition of the infant gut microbiota. It has been shown that a healthy infant gut microbiome is characterized by a low microbial diversity, with abundance of Bifidobacterium, Bacteroidetes, Firmicutes,... + info
Stehlikova Z, Kostovcikova K, Kverka M, Rossmann P, Dvorak J, Novosadova I, Kostovcik M, Coufal S, Srutkova D, Prochazkova P, Hudcovic T, Kozakova H, Stepankova R, Rob F, Juzlova K, Hercogova J, Tlaskalova-Hogenova H, Jiraskova Zakostelska Z. Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00236.
COMMENT: Psoriasis is a chronic inflammatory disease in which Th17 cells play a crucial role. It is well stablished that skin microbiota is involved in psoriasis induction and pathogenesis. Oral administration of a broad-spectrum antibiotic... + info
Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota.
Liang Y, Zhan J, Liu D, Luo M, Han J, Liu X, Liu C, Cheng Z, Zhou Z, Wang P. Microbiome. Feb 2019. doi: 10.1186/s40168-019-0635-4.
COMMENT: This work investigates the effects of a widely used pesticide on gut microbiota and obesity. Previous studies have detected this pesticide in food, and have found that in animals can develop obesity and other disorders. In this study, the... + info
Zorz J, Willis C, Comeau AM, Langille MGI, Johnson CL, Li WKW, LaRoche J. Front Microbiol. 2019. doi: 10.3389/fmicb.2019.00281.
The authors of this study analyzed the effects of physicochemical gradients on bacterial community structure. They sequenced the V6V8 hypervariable region of the 16S rRNA gene to characterize the bacterial community of the Scotian Shelf sector of... + info
Gogokhia L, Buhrke K, Bell R, Hoffman B, Brown DG, Hanke-Gogokhia C, Ajami NJ, Wong MC, Ghazaryan A, Valentine JF, Porter N, Martens E, O'Connell R, Jacob V, Scherl E, Crawford C, Stephens WZ, Casjens SR, Longman RS, Round JL. Cell Host Microbe. 02 2019.
COMMENT: Previous studies have shown that Bacteriophages are members of the resident gastrointestinal (GI) microbiota, and their composition is significantly different in individuals with inflammatory bowel disease (IBD) compared to healthy controls.... + info
Gut microbiome patterns correlate with higher postoperative complication rates after pancreatic surgery.
Schmitt FCF, Brenner T, Uhle F, Loesch S, Hackert T, Ulrich A, Hofer S, Dalpke AH, Weigand MA, Boutin S. BMC Microbiol. Feb 2019. doi: 10.1186/s12866-019-1399-5.
COMMENT: Postoperative complications are an important problem in clinical practice. This works investigates the influence of the gut microbiome in the postoperative clinical course of pancreatic surgery and its potential complications, by 16S rRNA... + info
16S rRNA amplicon sequencing characterization of caecal microbiome composition of broilers and free-range slow-growing chickens throughout their productive lifespan.
Ocejo M, Oporto B, Hurtado A. Sci Rep. Feb 2019. doi: 10.1038/s41598-019-39323-x.
COMMENT: Chickens are major source of food and protein worldwide. Feed conversion and the health of chickens relies on the complex microbial community that inhabits the chicken gut, including the ceca. By 16S rRNA high throughput sequencing,... + info
Analytical and clinical validation of a microbial cell-free DNA sequencing test for infectious disease.
Blauwkamp TA, Thair S, Rosen MJ, Blair L, Lindner MS, Vilfan ID, Kawli T, Christians FC, Venkatasubrahmanyam S, Wall GD, Cheung A, Rogers ZN, Meshulam-Simon G, Huijse L, Balakrishnan S, Quinn JV, Hollemon D, Hong DK, Vaughn ML, Kertesz M, Bercovici S, Wilber JC, Yang S. Nat Microbiol. Feb 2019. doi: 10.1038/s41564-018-0349-6.
COMMENT: This work shows the potential use of next-generation sequencing of cell-free DNA (cfDNA) from pathogens for clinical infectious disease testing. The Karius test isolates cfDNA from blood plasma, cfDNA is sequenced on Illumina NextSeq500 using... + info
Jin C, Lagoudas GK, Zhao C, Bullman S, Bhutkar A, Hu B, Ameh S, Sandel D, Liang XS, Mazzilli S, Whary MT, Meyerson M, Germain R, Blainey PC, Fox JG, Jacks T. Cell. Feb 2019.
Wilson MR, Jiang Y, Villalta PW, Stornetta A, Boudreau PD, Carrá A, Brennan CA, Chun E, Ngo L, Samson LD, Engelward BP, Garrett WS, Balbo S, Balskus EP. Science. 02 2019.
COMMENT: This study reveals that the genotoxin colibactin from E. coli present in the gut alkylates DNA in vivo and might contribute colorectal cancer development and progression. + info
The role of the microbiome in immunologic development and its implication for pancreatic cancer immunotherapy.
Sethi V, Vitiello GA, Saxena D, Miller G, Dudeja V. Gastroenterology. Feb 2019.
COMMENT: Review on the relation of microbiome and the immune system and the importance of it in the context of pacreatic cancer and cancer immunotherapy. + info
A Haemophilus sp. dominates the microbiota of sputum from UK adults with non-severe community acquired pneumonia and chronic lung disease.
Wootton DG, Cox MJ, Gloor GB, Litt D, Hoschler K, German E, Court J, Eneje O, Keogan L, Macfarlane L, Wilks S, Diggle PJ, Woodhead M, Moffatt MF, Cookson WOC, Gordon SB. Sci Rep. Feb 2019. doi: 10.1038/s41598-018-38090-5.
COMMENT: Community-acquired pneumonia (CAP) is one of the most common infectious diseases and is an important cause of mortality and morbidity worldwide. The bacterial aetiology of CAP is unclear because of the practical difficulties in obtaining... + info
Little cigars and cigarillos harbor diverse bacterial communities that differ between the tobacco and the wrapper.
Chattopadhyay S, Smyth EM, Kulkarni P, Babik KR, Reid M, Hittle LE, Clark PI, Mongodin EF, Sapkota AR. PLoS One. 2019. doi: 10.1371/journal.pone.0211705.
COMMENT: The bacterial diversity of little cigars and cigarillos is pretty unknown.The authors of this study analyzed the tobacco and wrappers of cigars and cigarillos of four different brands and characterized their bacterial community composition.... + info
Shkoporov AN, Hill C. Cell Host Microbe. Feb 2019.
COMMENT: In this review, the authors summarize the taxonomic composition, dynamics, and spatial structure of the human gut phageome, they also review the available methods and challenges associated with metagenomic analysis pipelines and future research... + info
Microbiome of drinking water: A full-scale spatio-temporal study to monitor water quality in the Paris distribution system.
Perrin Y, Bouchon D, Delafont V, Moulin L, Héchard Y. Water Res. Feb 2019.
COMMENT: This study used high-throughput sequencing (HTS) to analyze the microbiome of a large drinking water distribution system over a one-year period of time, the HTS-based method was compared with a culture-based method. The paper shows the sensitivity... + info
Characterization of oral microbiota in marmosets: Feasibility of using the marmoset as a human oral disease model.
Takehara S, Zeredo JL, Kumei Y, Kagiyama K, Fukasawa K, Oshiro A, Ueno M, Kojimahara N, Minakuchi S, Kawaguchi Y. PLoS One. 2019. doi: 10.1371/journal.pone.0207560.
COMMENT: Marmoset could be used as an animal model for the study of human oral health. Its dental physiology and relatively short life-span and relatively small size make the marmoset a better animal model over other non-human primates. + info
Frequency of disturbance alters diversity, function, and underlying assembly mechanisms of complex bacterial communities.
Santillan E, Seshan H, Constancias F, Drautz-Moses DI, Wuertz S. NPJ Biofilms Microbiomes. 2019. doi: 10.1038/s41522-019-0079-4.
COMMENT: The authors tested the effect of disturbances on the structure, assembly and function of complex microbial communities. For that, they added toxic 3-choroaniline as disturbance to complex microbial communities within an engineered system... + info
The Glucoamylase Inhibitor Acarbose Has a Diet-Dependent and Reversible Effect on the Murine Gut Microbiome.
Baxter NT, Lesniak NA, Sinani H, Schloss PD, Koropatkin NM. mSphere. 02 2019.
COMMENT: A safe and effective treatment for type 2 diabetes and prediabetes is the oral administration of acarbose, an inhibitor of the host (gluco)amylases of the small intestine. This inhibition prevent starch digestion in the small intestine, decreasing... + info
Metagenomic and metatranscriptomic analysis of human prostate microbiota from patients with prostate cancer.
Feng Y, Ramnarine VR, Bell R, Volik S, Davicioni E, Hayes VM, Ren S, Collins CC. BMC Genomics. Feb 2019. doi: 10.1186/s12864-019-5457-z.
COMMENT: The authors analyze the prostate microbiome of tumoral and benign adjacent tissue of 65 prostate cancer patients by means of metagenomics and metatranscriptomics. Even though the authors do not find strong correlations between prostate microbiome... + info
Effects of dietary fat on gut microbiota and faecal metabolites, and their relationship with cardiometabolic risk factors: a 6-month randomised controlled-feeding trial.
Wan Y, Wang F, Yuan J, Li J, Jiang D, Zhang J, Li H, Wang R, Tang J, Huang T, Zheng J, Sinclair AJ, Mann J, Li D. Gut. Feb 2019.
COMMENT: In most developping countries, the rates of obesity and other cardiometabolic disorders suchs as type 2 diabetes and cardiovascular diseases have increased rapidly in parallel with a transition from a lower-fat diet to a lower... + info
Saito K, Koido S, Odamaki T, Kajihara M, Kato K, Horiuchi S, Adachi S, Arakawa H, Yoshida S, Akasu T, Ito Z, Uchiyama K, Saruta M, Xiao JZ, Sato N, Ohkusa T. PLoS One. 2019. doi: 10.1371/journal.pone.0212406.
COMMENT: By means of sequencing analysis of the V3-V4 region of the 16S gene from colonoscopy aspirates the authors analize the gut microbiome diversity and disbiosis in patients with colorectal adenoma (CRA) or intramucosal colorectal carcinoma (CRC)... + info
Chien AL, Tsai J, Leung S, Mongodin EF, Nelson AM, Kang S, Garza LA. JAMA Dermatol. Feb 2019. doi: 10.1001/jamadermatol.2018.5221.
COMMENT: This pilot study investigated the association of systemic antibiotic treatment with acne severity and skin microbiota. The skin bacterial community of four women who had received a recent diagnosis of acne and were treated minocycline was... + info
Sanna S, van Zuydam NR, Mahajan A, Kurilshikov A, Vich Vila A, Võsa U, Mujagic Z, Masclee AAM, Jonkers DMAE, Oosting M, Joosten LAB, Netea MG, Franke L, Zhernakova A, Fu J, Wijmenga C, McCarthy MI. Nat Genet. Feb 2019. doi: 10.1038/s41588-019-0350-x.
COMMENT: This work provides a new workflow, based on Mendelian Randomization (MR) methods, that is able to integrate GWAS, microbiome and metabolic results to obtain causal inferences. This methodology is applied to the study of the relationships... + info
Reimer RA. Nat Rev Gastroenterol Hepatol. Feb 2019. doi: 10.1038/s41575-018-0093-7.
COMMENT: This work reviews the most important findings about the impact of diet in the demonstrated relationship between gut microbiome and disease, especially focusing to obesity, diabetes and metabolic syndrome. + info
Granado-Serrano AB, Martín-Garí M, Sánchez V, Riart Solans M, Berdún R, Ludwig IA, Rubió L, Vilaprinyó E, Portero-Otín M, Serrano JCE. Sci Rep. Feb 2019. doi: 10.1038/s41598-019-38874-3.
COMMENT: Hypercholesterolemia is an important risk factor of Cardiovascular diseases. Studies in mice have suggested that gut microbiota may affect lipid metabolism through bacterial metabolic products such as, short chain fatty acids (SCFAs), or... + info
Analysis of Pseudomonas aeruginosa biofilm membrane vesicles supports multiple mechanisms of biogenesis.
Cooke AC, Nello AV, Ernst RK, Schertzer JW. PLoS One. 2019. doi: 10.1371/journal.pone.0212275.
COMMENT: Bacterial Outer Membrane Vesicles (OMVs) naturally exist in Gram-negative bacteria. They play a critical role in the bacteria-bacteria and bateria-host interactions and have been implicated in biofilm development. To assess the OMV structure,... + info
Fraga CG, Croft KD, Kennedy DO, Tomás-Barberán FA. Food Funct. Feb 2019. doi: 10.1039/c8fo01997e.
COMMENT: The aim of this review is to explore how polyphenols exert health benefits in humans, and the role of gut microbiota in their metabolism to generate active metabolites. The polyphenols are a group of compounds found in plants. Food sources... + info
Conrads G, Abdelbary MMH. Anaerobe. Feb 2019.
COMMENT: Next generation sequencing is currently the method of choice for analyzing complex microbial communities. As a culture-independent method, it is specially useful for the study of anaerobes and anaerobic infections. However, results obtained... + info
Biofilm contamination of high-touched surfaces in intensive care units: epidemiology and potential impacts.
de Melo Costa D, Johani K, Melo DS, de Oliveira Lopes LK, de Oliveira Lopes Lima LK, Tipple AFV, Hu H, Vickery K. Lett Appl Microbiol. Feb 2019. doi: 10.1111/lam.13127.
COMMENT: Healthcare-associated infections are a public health problem in hospitals, particularly in intensive care units (ICUs). Previous studies have demonstrated the presence of viable microorganisms on hospital surfaces, especially in the frequently... + info
Impact of chronic dietary red meat, white meat, or non-meat protein on trimethylamine N-oxide metabolism and renal excretion in healthy men and women.
Wang Z, Bergeron N, Levison BS, Li XS, Chiu S, Jia X, Koeth RA, Li L, Wu Y, Tang WHW, Krauss RM, Hazen SL. Eur Heart J. Feb 2019. doi: 10.1093/eurheartj/ehy799.
COMMENT: This work is focused on Trimethylamine N-oxide (TMAO). TMAO is a metabolite generated by gut microbiome that has been linked to the pathogenesis of atherosclerotic heart disease. A randomized 2-arm (high- or low-saturated fat) crossover... + info
Quinn RA, Adem S, Mills RH, Comstock W, DeRight Goldasich L, Humphrey G, Aksenov AA, Melnik AV, da Silva R, Ackermann G, Bandeira N, Gonzalez DJ, Conrad D, O'Donoghue AJ, Knight R, Dorrestein PC. Microbiome. Feb 2019. doi: 10.1186/s40168-019-0636-3.
COMMENT: In this work the microbial and molecular composition of sputum samples from Cystic Fibrosis (CF) patients are analyzed using 16S rRNA gene amplicon sequencing and mass spectrometry to analyze metabolites. The integration of these 2 types... + info
Bradley P, den Bakker HC, Rocha EPC, McVean G, Iqbal Z. Nat Biotechnol. Feb 2019. doi: 10.1038/s41587-018-0010-1.
COMMENT: This article describes a new method called BIGSI for storing and searching large nucleotide sequence databases. The new method is based on the use of Sequence Bloom Trees that were previously used for the detection of specific transcripts... + info
Dopamine Is a Siderophore-Like Iron Chelator That Promotes Salmonella enterica Serovar Typhimurium Virulence in Mice.
Dichtl S, Demetz E, Haschka D, Tymoszuk P, Petzer V, Nairz M, Seifert M, Hoffmann A, Brigo N, Würzner R, Theurl I, Karlinsey JE, Fang FC, Weiss G. MBio. Feb 2019.
COMMENT: This work can have an important impact in septic shock produced by Salmonella since it reports that dopamine, used in septic shock treatment, promotes Salmonella virulence because acts as siderophore-like iron chelator that stimulates bacterial... + info
The gut microbiome from patients with schizophrenia modulates the glutamate-glutamine-GABA cycle and schizophrenia-relevant behaviors in mice
Zheng P et al. Science Advances. Vol. 5, no. 2, eaau8317.
COMMENT: This work analyzes possible relationships between the gut microbiome from patients with schizophrenia (SCZ) and the schizophrenic... + info
Forster SC, Kumar N, Anonye BO, Almeida A, Viciani E, Stares MD, Dunn M, Mkandawire TT, Zhu A, Shao Y, Pike LJ, Louie T, Browne HP, Mitchell AL, Neville BA, Finn RD, Lawley TD. Nat Biotechnol. Feb 2019. doi: 10.1038/s41587-018-0009-7.
COMMENT: The authors present the Human Gastrointestinal Bacteria Culture Collection (HBC). A collection of 737 bacterial genomes from 273 species from human gastrointestinal microbiome and the corresponding isolates. Both the sequence data and the... + info
Zou Y, Xue W, Luo G, Deng Z, Qin P, Guo R, Sun H, Xia Y, Liang S, Dai Y, Wan D, Jiang R, Su L, Feng Q, Jie Z, Guo T, Xia Z, Liu C, Yu J, Lin Y, Tang S, Huo G, Xu X, Hou Y, Liu X, Wang J, Yang H, Kristiansen K, Li J, Jia H, Xiao L. Nat Biotechnol. Feb 2019. doi: 10.1038/s41587-018-0008-8.
COMMENT: 1,520 draft reference genomes of culturable bacteria from human gut microbiomes from healthy donors. + info
Mesa F, Magan-Fernandez A, Castellino G, Chianetta R, Nibali L, Rizzo M. Biochim Biophys Acta Mol Basis Dis. Feb 2019.
COMMENT: The authors in this review article summarize the current knowledge of the influence of the periodontitis in the development of the cardiovascular disease. They review recent epidemiological studies that support the association of the periodontitis... + info
Valles-Colomer M, Falony G, Darzi Y, Tigchelaar EF, Wang J, Tito RY, Schiweck C, Kurilshikov A, Joossens M, Wijmenga C, Claes S, Van Oudenhove L, Zhernakova A, Vieira-Silva S, Raes J. Nat Microbiol. Feb 2019. doi: 10.1038/s41564-018-0337-x.
COMMENT: This work is focused to the neuroactive potential of the human gut microbiome and is centered in studying how microbiome features correlate with host quality of life and depression. The findings of this work add new support for the importance... + info
Sarin SK, Pande A, Schnabl B. J Hepatol. Feb 2019.
COMMENT: Modulation of gut microbial composition by faecal microbiota transplantation or precision microbiome therapies are the new therapeutic options which are currently being evaluated for patients with alcohol-related liver disease. + info