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










  • Quantifying the contribution of microbial immigration in engineered water systems.

    abstract::Immigration is a process that can influence the assembly of microbial communities in natural and engineered environments. However, it remains challenging to quantitatively evaluate the contribution of this process to the microbial diversity and function in the receiving ecosystems. Currently used methods, i.e., counti...


    pub_type: 杂志文章,评审


    authors: Mei R,Liu WT

    更新日期:2019-11-06 00:00:00

  • Tracking microbial colonization in fecal microbiota transplantation experiments via genome-resolved metagenomics.

    abstract:BACKGROUND:Fecal microbiota transplantation (FMT) is an effective treatment for recurrent Clostridium difficile infection and shows promise for treating other medical conditions associated with intestinal dysbioses. However, we lack a sufficient understanding of which microbial populations successfully colonize the rec...


    pub_type: 杂志文章


    authors: Lee STM,Kahn SA,Delmont TO,Shaiber A,Esen ÖC,Hubert NA,Morrison HG,Antonopoulos DA,Rubin DT,Eren AM

    更新日期:2017-05-04 00:00:00

  • Environmental toxicants in breast milk of Norwegian mothers and gut bacteria composition and metabolites in their infants at 1 month.

    abstract:BACKGROUND:Early disruption of the microbial community may influence life-long health. Environmental toxicants can contaminate breast milk and the developing infant gut microbiome is directly exposed. We investigated whether environmental toxicants in breastmilk affect the composition and function of the infant gut mic...


    pub_type: 杂志文章


    authors: Iszatt N,Janssen S,Lenters V,Dahl C,Stigum H,Knight R,Mandal S,Peddada S,González A,Midtvedt T,Eggesbø M

    更新日期:2019-02-27 00:00:00

  • Hybridization capture reveals microbial diversity missed using current profiling methods.

    abstract:BACKGROUND:Microorganisms comprise the majority of living organisms on our planet. For many years, exploration of the composition of microbial communities has been performed through the PCR-based study of the small subunit rRNA gene due to its high conservation across the domains of life. The application of this method...


    pub_type: 杂志文章


    authors: Gasc C,Peyret P

    更新日期:2018-03-27 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

  • Specific gut microbiome members are associated with distinct immune markers in pediatric allogeneic hematopoietic stem cell transplantation.

    abstract:BACKGROUND:Increasing evidence reveals the importance of the microbiome in health and disease and inseparable host-microbial dependencies. Host-microbe interactions are highly relevant in patients receiving allogeneic hematopoietic stem cell transplantation (HSCT), i.e., a replacement of the cellular components of the ...


    pub_type: 杂志文章


    authors: Ingham AC,Kielsen K,Cilieborg MS,Lund O,Holmes S,Aarestrup FM,Müller KG,Pamp SJ

    更新日期:2019-09-13 00:00:00

  • Relative and contextual contribution of different sources to the composition and abundance of indoor air bacteria in residences.

    abstract:BACKGROUND:The study of the microbial communities in the built environment is of critical importance as humans spend the majority of their time indoors. While the microorganisms in living spaces, especially those in the air, can impact health and well-being, little is known of their identity and the processes that dete...


    pub_type: 杂志文章


    authors: Miletto M,Lindow SE

    更新日期:2015-12-10 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

  • The vaginal microbiota, human papillomavirus infection and cervical intraepithelial neoplasia: what do we know and where are we going next?

    abstract::The vaginal microbiota plays a significant role in health and disease of the female reproductive tract. Next-generation sequencing techniques based upon the analysis of bacterial 16S rRNA genes permit in-depth study of vaginal microbial community structure to a level of detail not possible with standard culture-based ...


    pub_type: 杂志文章,评审


    authors: Mitra A,MacIntyre DA,Marchesi JR,Lee YS,Bennett PR,Kyrgiou M

    更新日期:2016-11-01 00:00:00

  • Niche differentiation rather than biogeography shapes the diversity and composition of microbiome of Cycas panzhihuaensis.

    abstract:BACKGROUND:Given their adaptation to nutrient-poor and drought environments, cycads are vital models for plant-microbiome interaction research because they are likely to host an important reservoir of beneficial microbes that may support cycad survival. However, a comprehensive understanding of the diversity and commun...


    pub_type: 杂志文章


    authors: Zheng Y,Gong X

    更新日期:2019-12-02 00:00:00

  • Bloom and bust: intestinal microbiota dynamics in response to hospital exposures and Clostridium difficile colonization or infection.

    abstract:BACKGROUND:Clostridium difficile infection (CDI) is the leading infectious cause of nosocomial diarrhea. Hospitalized patients are at increased risk of developing CDI because they are exposed to C. difficile spores through contact with the hospital environment and often receive antibiotics and other medications that ca...


    pub_type: 杂志文章


    authors: Vincent C,Miller MA,Edens TJ,Mehrotra S,Dewar K,Manges AR

    更新日期:2016-03-14 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

  • MetaCHIP: community-level horizontal gene transfer identification through the combination of best-match and phylogenetic approaches.

    abstract:BACKGROUND:Metagenomic datasets provide an opportunity to study horizontal gene transfer (HGT) on the level of a microbial community. However, current HGT detection methods cannot be applied to community-level datasets or require reference genomes. Here, we present MetaCHIP, a pipeline for reference-independent HGT ide...


    pub_type: 杂志文章


    authors: Song W,Wemheuer B,Zhang S,Steensen K,Thomas T

    更新日期:2019-03-04 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

  • Humans as holobionts: implications for prevention and therapy.

    abstract::The human gut microbiota is increasingly recognized for its important or even decisive role in health. As it becomes clear that microbiota and host mutually affect and depend on each other in an intimate relationship, a holistic view of the gut microbiota-host association imposes itself. Ideally, a stable state of equ...


    pub_type: 杂志文章,评审


    authors: van de Guchte M,Blottière HM,Doré J

    更新日期:2018-05-01 00:00:00

  • Transplanted human fecal microbiota enhanced Guillain Barré syndrome autoantibody responses after Campylobacter jejuni infection in C57BL/6 mice.

    abstract:BACKGROUND:Campylobacter jejuni is the leading antecedent infection to the autoimmune neuropathy Guillain-Barré syndrome (GBS), which is accompanied by an autoimmune anti-ganglioside antibody attack on peripheral nerves. Previously, we showed that contrasting immune responses mediate C. jejuni induced colitis and autoi...


    pub_type: 杂志文章


    authors: Brooks PT,Brakel KA,Bell JA,Bejcek CE,Gilpin T,Brudvig JM,Mansfield LS

    更新日期:2017-08-08 00:00:00

  • Ruminal microbiome-host crosstalk stimulates the development of the ruminal epithelium in a lamb model.

    abstract:BACKGROUND:The development of the rumen is an important physiological challenge for young ruminants. Previous studies have shown that starter feeding can effectively facilitate the growth and development of the rumen in ruminants. However, the mechanism through which starter feeding stimulates the development of the ru...


    pub_type: 杂志文章


    authors: Lin L,Xie F,Sun D,Liu J,Zhu W,Mao S

    更新日期:2019-06-03 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

  • 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

  • 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

  • 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

  • Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis.

    abstract:BACKGROUND:Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the ge...


    pub_type: 杂志文章


    authors: Hammond M,Homa F,Andersson-Svahn H,Ettema TJ,Joensson HN

    更新日期:2016-10-06 00:00:00

  • Apple endophytic microbiota of different rootstock/scion combinations suggests a genotype-specific influence.

    abstract:BACKGROUND:High-throughput amplicon sequencing spanning conserved portions of microbial genomes (16s rRNA and ITS) was used in the present study to describe the endophytic microbiota associated with three apple varieties, "Royal Gala," "Golden Delicious," and "Honey Crisp," and two rootstocks, M.9 and M.M.111. The obje...


    pub_type: 杂志文章


    authors: Liu J,Abdelfattah A,Norelli J,Burchard E,Schena L,Droby S,Wisniewski M

    更新日期:2018-01-27 00:00:00

  • The human gut archaeome: identification of diverse haloarchaea in Korean subjects.

    abstract:BACKGROUND:Archaea are one of the least-studied members of the gut-dwelling autochthonous microbiota. Few studies have reported the dominance of methanogens in the archaeal microbiome (archaeome) of the human gut, although limited information regarding the diversity and abundance of other archaeal phylotypes is availab...


    pub_type: 杂志文章


    authors: Kim JY,Whon TW,Lim MY,Kim YB,Kim N,Kwon MS,Kim J,Lee SH,Choi HJ,Nam IH,Chung WH,Kim JH,Bae JW,Roh SW,Nam YD

    更新日期:2020-08-04 00:00:00

  • Organophosphorus pesticide chlorpyrifos intake promotes obesity and insulin resistance through impacting gut and gut microbiota.

    abstract:BACKGROUND:Disruption of the gut microbiota homeostasis may induce low-grade inflammation leading to obesity-associated diseases. A major protective mechanism is to use the multi-layered mucus structures to keep a safe distance between gut epithelial cells and microbiota. To investigate whether pesticides would induce ...


    pub_type: 杂志文章


    authors: Liang Y,Zhan J,Liu D,Luo M,Han J,Liu X,Liu C,Cheng Z,Zhou Z,Wang P

    更新日期:2019-02-11 00:00:00

  • The unsolved problem of otitis media in indigenous populations: a systematic review of upper respiratory and middle ear microbiology in indigenous children with otitis media.

    abstract:BACKGROUND:Otitis media (OM) imposes a great burden of disease in indigenous populations around the world, despite a variety of treatment and prevention programs. Improved understanding of the pathogenesis of OM in indigenous populations is required to advance treatment and reduce prevalence. We conducted a systematic ...


    pub_type: 杂志文章


    authors: Coleman A,Wood A,Bialasiewicz S,Ware RS,Marsh RL,Cervin A

    更新日期:2018-11-05 00:00:00

  • Genomic insights into potential interdependencies in microbial hydrocarbon and nutrient cycling in hydrothermal sediments.

    abstract:BACKGROUND:Deep-sea hydrothermal vents are hotspots for productivity and biodiversity. Thermal pyrolysis and circulation produce fluids rich in hydrocarbons and reduced compounds that stimulate microbial activity in surrounding sediments. Several studies have characterized the diversity of Guaymas Basin (Gulf of Califo...


    pub_type: 杂志文章


    authors: Dombrowski N,Seitz KW,Teske AP,Baker BJ

    更新日期:2017-08-23 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

  • Re-evaluating the relationship between missing heritability and the microbiome.

    abstract::Human genome-wide association studies (GWASs) have recurrently estimated lower heritability estimates than familial studies. Many explanations have been suggested to explain these lower estimates, including that a substantial proportion of genetic variation and gene-by-environment interactions are unmeasured in typica...


    pub_type: 信件


    authors: Douglas GM,Bielawski JP,Langille MGI

    更新日期:2020-06-08 00:00:00

  • Wild bees and their nests host Paenibacillus bacteria with functional potential of avail.

    abstract:BACKGROUND:In previous studies, the gram-positive firmicute genus Paenibacillus was found with significant abundances in nests of wild solitary bees. Paenibacillus larvae is well-known for beekeepers as a severe pathogen causing the fatal honey bee disease American foulbrood, and other members of the genus are either s...


    pub_type: 杂志文章


    authors: Keller A,Brandel A,Becker MC,Balles R,Abdelmohsen UR,Ankenbrand MJ,Sickel W

    更新日期:2018-12-22 00:00:00