Context and the human microbiome.


:Human microbiome reference datasets provide epidemiological context for researchers, enabling them to uncover new insights into their own data through meta-analyses. In addition, large and comprehensive reference sets offer a means to develop or test hypotheses and can pave the way for addressing practical study design considerations such as sample size decisions. We discuss the importance of reference sets in human microbiome research, limitations of existing resources, technical challenges to employing reference sets, examples of their usage, and contributions of the American Gut Project to the development of a comprehensive reference set. Through engaging the general public, the American Gut Project aims to address many of the issues present in existing reference resources, characterizing health and disease, lifestyle, and dietary choices of the participants while extending its efforts globally through international collaborations.






McDonald D,Birmingham A,Knight R




Has Abstract


2015-11-04 00:00:00










  • Microbiome for Mars: surveying microbiome connections to healthcare with implications for long-duration human spaceflight, virtual workshop, July 13, 2020.

    abstract::The inaugural "Microbiome for Mars" virtual workshop took place on July 13, 2020. This event assembled leaders in microbiome research and development to discuss their work and how it may relate to long-duration human space travel. The conference focused on surveying current microbiome research, future endeavors, and h...


    pub_type: 杂志文章


    authors: LaPelusa M,Donoviel D,Branzini SE,Carlson PE Jr,Culler S,Cheema AK,Kaddurah-Daouk R,Kelly D,de Cremoux I,Knight R,Krajmalnik-Brown R,Mayo SL,Mazmanian SK,Mayer EA,Petrosino JF,Garrison K

    更新日期:2021-01-04 00:00:00

  • Two sampling methods yield distinct microbial signatures in the nasopharynges of asthmatic children.

    abstract:BACKGROUND:The nasopharynx is a reservoir for pathogens associated with respiratory illnesses, such as asthma. Next-generation sequencing (NGS) has been used to characterize the nasopharyngeal microbiome during health and disease. Most studies so far have surveyed the nasopharynx as a whole; however, less is known abou...


    pub_type: 杂志文章


    authors: Pérez-Losada M,Crandall KA,Freishtat RJ

    更新日期:2016-06-16 00:00:00

  • Pre-pregnancy weight, gestational weight gain, and the gut microbiota of mothers and their infants.

    abstract:BACKGROUND:Recent evidence supports that the maternal gut microbiota impacts the initial infant gut microbiota. Since the gut microbiota may play a causal role in the development of obesity, it is important to understand how pre-pregnancy weight and gestational weight gain (GWG) impact the gut microbiota of mothers at ...


    pub_type: 杂志文章


    authors: Stanislawski MA,Dabelea D,Wagner BD,Sontag MK,Lozupone CA,Eggesbø M

    更新日期:2017-09-04 00:00:00

  • Rhizosphere microbiomes diverge among Populus trichocarpa plant-host genotypes and chemotypes, but it depends on soil origin.

    abstract:BACKGROUND:Plants have developed defense strategies for phytopathogen and herbivore protection via coordinated metabolic mechanisms. Low-molecular weight metabolites produced within plant tissues, such as salicylic acid, represent one such mechanism which likely mediates plant - microbe interactions above and below gro...


    pub_type: 杂志文章


    authors: Veach AM,Morris R,Yip DZ,Yang ZK,Engle NL,Cregger MA,Tschaplinski TJ,Schadt CW

    更新日期:2019-05-18 00:00:00

  • Bacteriophage-prokaryote dynamics and interaction within anaerobic digestion processes across time and space.

    abstract:BACKGROUND:Bacteriophage-prokaryote dynamics and interaction are believed to be important in governing microbiome composition and ecosystem functions, yet our limited knowledge of the spatial and temporal variation in phage and prokaryotic community compositions precludes accurate assessment of their roles and impacts....


    pub_type: 杂志文章


    authors: Zhang J,Gao Q,Zhang Q,Wang T,Yue H,Wu L,Shi J,Qin Z,Zhou J,Zuo J,Yang Y

    更新日期:2017-05-31 00:00:00

  • Host genetic variation in mucosal immunity pathways influences the upper airway microbiome.

    abstract:BACKGROUND:The degree to which host genetic variation can modulate microbial communities in humans remains an open question. Here, we performed a genetic mapping study of the microbiome in two accessible upper airway sites, the nasopharynx and the nasal vestibule, during two seasons in 144 adult members of a founder po...


    pub_type: 杂志文章


    authors: Igartua C,Davenport ER,Gilad Y,Nicolae DL,Pinto J,Ober C

    更新日期:2017-02-01 00:00:00

  • An integrated meta-omics approach reveals substrates involved in synergistic interactions in a bisphenol A (BPA)-degrading microbial community.

    abstract:BACKGROUND:Understanding microbial interactions in engineering bioprocesses is important to enhance and optimize performance outcomes and requires dissection of the multi-layer complexities of microbial communities. However, unraveling microbial interactions as well as substrates involved in complex microbial communiti...


    pub_type: 杂志文章


    authors: Yu K,Yi S,Li B,Guo F,Peng X,Wang Z,Wu Y,Alvarez-Cohen L,Zhang T

    更新日期:2019-02-06 00:00:00

  • The chicken gut metagenome and the modulatory effects of plant-derived benzylisoquinoline alkaloids.

    abstract:BACKGROUND:Sub-therapeutic antibiotics are widely used as growth promoters in the poultry industry; however, the resulting antibiotic resistance threatens public health. A plant-derived growth promoter, Macleaya cordata extract (MCE), with effective ingredients of benzylisoquinoline alkaloids, is a potential alternativ...


    pub_type: 杂志文章


    authors: Huang P,Zhang Y,Xiao K,Jiang F,Wang H,Tang D,Liu D,Liu B,Liu Y,He X,Liu H,Liu X,Qing Z,Liu C,Huang J,Ren Y,Yun L,Yin L,Lin Q,Zeng C,Su X,Yuan J,Lin L,Hu N,Cao H,Huang S,Guo Y,Fan W,Zeng J

    更新日期:2018-11-27 00:00:00

  • Optimal screening and donor management in a public stool bank.

    abstract:BACKGROUND:Fecal microbiota transplantation is an effective treatment for recurrent Clostridium difficile infection and is being investigated as a treatment for other microbiota-associated diseases. To facilitate these activities, an international public stool bank has been created, which screens donors and processes s...


    pub_type: 杂志文章


    authors: Kazerouni A,Burgess J,Burns LJ,Wein LM

    更新日期:2015-12-17 00:00:00

  • Novel facultative Methylocella strains are active methane consumers at terrestrial natural gas seeps.

    abstract:BACKGROUND:Natural gas seeps contribute to global climate change by releasing substantial amounts of the potent greenhouse gas methane and other climate-active gases including ethane and propane to the atmosphere. However, methanotrophs, bacteria capable of utilising methane as the sole source of carbon and energy, pla...


    pub_type: 杂志文章


    authors: Farhan Ul Haque M,Crombie AT,Murrell JC

    更新日期:2019-10-04 00:00:00

  • Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson's disease.

    abstract:BACKGROUND:Parkinson's disease (PD) is a neurodegenerative disorder with no absolute cure. The evidence of the involvement of gut microbiota in PD pathogenesis suggests the need to identify certain molecule(s) derived from the gut microbiota, which has the potential to manage PD. Osteocalcin (OCN), an osteoblast-secret...


    pub_type: 杂志文章


    authors: Hou YF,Shan C,Zhuang SY,Zhuang QQ,Ghosh A,Zhu KC,Kong XK,Wang SM,Gong YL,Yang YY,Tao B,Sun LH,Zhao HY,Guo XZ,Wang WQ,Ning G,Gu YY,Li ST,Liu JM

    更新日期:2021-01-31 00:00:00

  • Microbe observation and cultivation array (MOCA) for cultivating and analyzing environmental microbiota.

    abstract:BACKGROUND:The use of culture-independent nucleic acid techniques, such as ribosomal RNA gene cloning library analysis, has unveiled the tremendous microbial diversity that exists in natural environments. In sharp contrast to this great achievement is the current difficulty in cultivating the majority of bacterial spec...


    pub_type: 杂志文章


    authors: Gao W,Navarroli D,Naimark J,Zhang W,Chao SH,Meldrum DR

    更新日期:2013-01-09 00:00:00

  • The human gallbladder microbiome is related to the physiological state and the biliary metabolic profile.

    abstract:BACKGROUND:The microbial populations of the human intestinal tract and their relationship to specific diseases have been extensively studied during the last decade. However, the characterization of the human bile microbiota as a whole has been hampered by difficulties in accessing biological samples and the lack of ade...


    pub_type: 杂志文章


    authors: Molinero N,Ruiz L,Milani C,Gutiérrez-Díaz I,Sánchez B,Mangifesta M,Segura J,Cambero I,Campelo AB,García-Bernardo CM,Cabrera A,Rodríguez JI,González S,Rodríguez JM,Ventura M,Delgado S,Margolles A

    更新日期:2019-07-04 00:00:00

  • Gut-dependent microbial translocation induces inflammation and cardiovascular events after ST-elevation myocardial infarction.

    abstract:BACKGROUND:Post-infarction cardiovascular remodeling and heart failure are the leading cause of myocardial infarction (MI)-driven death during the past decades. Experimental observations have involved intestinal microbiota in the susceptibility to MI in mice; however, in humans, identifying whether translocation of gut...


    pub_type: 杂志文章


    authors: Zhou X,Li J,Guo J,Geng B,Ji W,Zhao Q,Li J,Liu X,Liu J,Guo Z,Cai W,Ma Y,Ren D,Miao J,Chen S,Zhang Z,Chen J,Zhong J,Liu W,Zou M,Li Y,Cai J

    更新日期:2018-04-03 00:00:00

  • The occurrence of potato common scab correlates with the community composition and function of the geocaulosphere soil microbiome.

    abstract:BACKGROUND:Soil microorganisms can mediate the occurrence of plant diseases. Potato common scab (CS) is a refractory disease caused by pathogenic Streptomyces that occurs worldwide, but little is known about the interactions between CS and the soil microbiome. In this study, four soil-root system compartments (geocaulo...


    pub_type: 杂志文章


    authors: Shi W,Li M,Wei G,Tian R,Li C,Wang B,Lin R,Shi C,Chi X,Zhou B,Gao Z

    更新日期:2019-02-01 00:00:00

  • Multi-cohort analysis of colorectal cancer metagenome identified altered bacteria across populations and universal bacterial markers.

    abstract:BACKGROUND:Alterations of gut microbiota are associated with colorectal cancer (CRC) in different populations and several bacterial species were found to contribute to the tumorigenesis. The potential use of gut microbes as markers for early diagnosis has also been reported. However, cohort specific noises may distort ...


    pub_type: 杂志文章


    authors: Dai Z,Coker OO,Nakatsu G,Wu WKK,Zhao L,Chen Z,Chan FKL,Kristiansen K,Sung JJY,Wong SH,Yu J

    更新日期:2018-04-11 00:00:00

  • VALENCIA: a nearest centroid classification method for vaginal microbial communities based on composition.

    abstract:BACKGROUND:Taxonomic profiles of vaginal microbial communities can be sorted into a discrete number of categories termed community state types (CSTs). This approach is advantageous because collapsing a hyper-dimensional taxonomic profile into a single categorical variable enables efforts such as data exploration, epide...


    pub_type: 杂志文章


    authors: France MT,Ma B,Gajer P,Brown S,Humphrys MS,Holm JB,Waetjen LE,Brotman RM,Ravel J

    更新日期:2020-11-23 00:00:00

  • Clustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease.

    abstract:BACKGROUND:Whole-genome "shotgun" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experim...


    pub_type: 杂志文章


    authors: Minot SS,Willis AD

    更新日期:2019-08-01 00:00:00

  • A metagenomic approach from aphid's hemolymph sheds light on the potential roles of co-existing endosymbionts.

    abstract:BACKGROUND:Aphids are known to live in symbiosis with specific bacteria, called endosymbionts which can be classified as obligate or accessory. Buchnera aphidicola is generally the only obligatory symbiont present in aphids, supplying essential nutrients that are missing in the plants phloem to its host. Pentalonia nig...


    pub_type: 杂志文章


    authors: De Clerck C,Fujiwara A,Joncour P,Léonard S,Félix ML,Francis F,Jijakli MH,Tsuchida T,Massart S

    更新日期:2015-12-15 00:00:00

  • The gut mycobiome of the Human Microbiome Project healthy cohort.

    abstract:BACKGROUND:Most studies describing the human gut microbiome in healthy and diseased states have emphasized the bacterial component, but the fungal microbiome (i.e., the mycobiome) is beginning to gain recognition as a fundamental part of our microbiome. To date, human gut mycobiome studies have primarily been disease c...


    pub_type: 杂志文章


    authors: Nash AK,Auchtung TA,Wong MC,Smith DP,Gesell JR,Ross MC,Stewart CJ,Metcalf GA,Muzny DM,Gibbs RA,Ajami NJ,Petrosino JF

    更新日期:2017-11-25 00:00:00

  • Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.

    abstract:BACKGROUND:Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs...


    pub_type: 杂志文章


    authors: Kwak S,Choi J,Hink T,Reske KA,Blount K,Jones C,Bost MH,Sun X,Burnham CD,Dubberke ER,Dantas G,CDC Prevention Epicenter Program.

    更新日期:2020-08-31 00:00:00

  • Consistent responses of soil microbial taxonomic and functional attributes to mercury pollution across China.

    abstract:BACKGROUND:The ecological consequences of mercury (Hg) pollution-one of the major pollutants worldwide-on microbial taxonomic and functional attributes remain poorly understood and largely unexplored. Using soils from two typical Hg-impacted regions across China, here, we evaluated the role of Hg pollution in regulatin...


    pub_type: 杂志文章


    authors: Liu YR,Delgado-Baquerizo M,Bi L,Zhu J,He JZ

    更新日期:2018-10-18 00:00:00

  • CopyRighter: a rapid tool for improving the accuracy of microbial community profiles through lineage-specific gene copy number correction.

    abstract:BACKGROUND:Culture-independent molecular surveys targeting conserved marker genes, most notably 16S rRNA, to assess microbial diversity remain semi-quantitative due to variations in the number of gene copies between species. RESULTS:Based on 2,900 sequenced reference genomes, we show that 16S rRNA gene copy number (GC...


    pub_type: 杂志文章


    authors: Angly FE,Dennis PG,Skarshewski A,Vanwonterghem I,Hugenholtz P,Tyson GW

    更新日期:2014-04-07 00:00:00

  • Dichotomous development of the gut microbiome in preterm infants.

    abstract:BACKGROUND:Preterm infants are at risk of developing intestinal dysbiosis with an increased proportion of Gammaproteobacteria. In this study, we sought the clinical determinants of the relative abundance of feces-associated Gammaproteobacteria in very low birth weight (VLBW) infants. Fecal microbiome was characterized ...


    pub_type: 杂志文章


    authors: Ho TTB,Groer MW,Kane B,Yee AL,Torres BA,Gilbert JA,Maheshwari A

    更新日期:2018-09-12 00:00:00

  • 16S rRNA gene-based profiling of the human infant gut microbiota is strongly influenced by sample processing and PCR primer choice.

    abstract:BACKGROUND:Characterisation of the bacterial composition of the gut microbiota is increasingly carried out with a view to establish the role of different bacterial species in causation or prevention of disease. It is thus essential that the methods used to determine the microbial composition are robust. Here, several w...


    pub_type: 杂志文章


    authors: Walker AW,Martin JC,Scott P,Parkhill J,Flint HJ,Scott KP

    更新日期:2015-06-22 00:00:00

  • Short-term consumption of a high-fat diet increases host susceptibility to Listeria monocytogenes infection.

    abstract:BACKGROUND:A westernized diet comprising a high caloric intake from animal fats is known to influence the development of pathological inflammatory conditions. However, there has been relatively little focus upon the implications of such diets for the progression of infectious disease. Here, we investigated the influenc...


    pub_type: 杂志文章


    authors: Las Heras V,Clooney AG,Ryan FJ,Cabrera-Rubio R,Casey PG,Hueston CM,Pinheiro J,Rudkin JK,Melgar S,Cotter PD,Hill C,Gahan CGM

    更新日期:2019-01-18 00:00:00

  • Diet shapes the gut microbiome of pigs during nursing and weaning.

    abstract:BACKGROUND:The newborn mammal is rapidly colonized by a complex microbial community, whose importance for host health is becoming increasingly clear. Understanding the forces that shape the early community, especially during the nursing period, is critical to gain insight into how this consortium of microbes is assembl...


    pub_type: 杂志文章


    authors: Frese SA,Parker K,Calvert CC,Mills DA

    更新日期:2015-07-01 00:00:00

  • Genomic characterization of the uncultured Bacteroidales family S24-7 inhabiting the guts of homeothermic animals.

    abstract:BACKGROUND:Our view of host-associated microbiota remains incomplete due to the presence of as yet uncultured constituents. The Bacteroidales family S24-7 is a prominent example of one of these groups. Marker gene surveys indicate that members of this family are highly localized to the gastrointestinal tracts of homeot...


    pub_type: 杂志文章


    authors: Ormerod KL,Wood DL,Lachner N,Gellatly SL,Daly JN,Parsons JD,Dal'Molin CG,Palfreyman RW,Nielsen LK,Cooper MA,Morrison M,Hansbro PM,Hugenholtz P

    更新日期:2016-07-07 00:00:00

  • Encrustations on ureteral stents from patients without urinary tract infection reveal distinct urotypes and a low bacterial load.

    abstract:BACKGROUND:Current knowledge of the urinary tract microbiome is limited to urine analysis and analysis of biofilms formed on Foley catheters. Bacterial biofilms on ureteral stents have rarely been investigated, and no cultivation-independent data are available on the microbiome of the encrustations on the stents. RESU...


    pub_type: 杂志文章


    authors: Buhmann MT,Abt D,Nolte O,Neu TR,Strempel S,Albrich WC,Betschart P,Zumstein V,Neels A,Maniura-Weber K,Ren Q

    更新日期:2019-04-13 00:00:00

  • Chemotherapy-induced oral mucositis is associated with detrimental bacterial dysbiosis.

    abstract:BACKGROUND:Gastrointestinal mucosal injury (mucositis), commonly affecting the oral cavity, is a clinically significant yet incompletely understood complication of cancer chemotherapy. Although antineoplastic cytotoxicity constitutes the primary injury trigger, the interaction of oral microbial commensals with mucosal ...


    pub_type: 杂志文章


    authors: Hong BY,Sobue T,Choquette L,Dupuy AK,Thompson A,Burleson JA,Salner AL,Schauer PK,Joshi P,Fox E,Shin DG,Weinstock GM,Strausbaugh LD,Dongari-Bagtzoglou A,Peterson DE,Diaz PI

    更新日期:2019-04-25 00:00:00