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 available. RESULTS:We surveyed the archaeome of faecal samples collected from 897 East Asian subjects living in South Korea. In total, 42.47% faecal samples were positive for archaeal colonisation; these were subsequently subjected to archaeal 16S rRNA gene deep sequencing and real-time quantitative polymerase chain reaction-based abundance estimation. The mean archaeal relative abundance was 10.24 ± 4.58% of the total bacterial and archaeal abundance. We observed extensive colonisation of haloarchaea (95.54%) in the archaea-positive faecal samples, with 9.63% mean relative abundance in archaeal communities. Haloarchaea were relatively more abundant than methanogens in some samples. The presence of haloarchaea was also verified by fluorescence in situ hybridisation analysis. Owing to large inter-individual variations, we categorised the human gut archaeome into four archaeal enterotypes. CONCLUSIONS:The study demonstrated that the human gut archaeome is indigenous, responsive, and functional, expanding our understanding of the archaeal signature in the gut of human individuals. Video Abstract.
journal_name
Microbiomejournal_title
Microbiomeauthors
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 YDdoi
10.1186/s40168-020-00894-xsubject
Has Abstractpub_date
2020-08-04 00:00:00pages
114issue
1issn
2049-2618pii
10.1186/s40168-020-00894-xjournal_volume
8pub_type
杂志文章相关文献
Microbiome文献大全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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0403-x
更新日期:2018-01-27 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0140-3
更新日期:2015-12-17 00:00:00
abstract:BACKGROUND:pH is frequently reported as the main driver for prokaryotic community structure in soils. However, pH changes are also linked to "spillover effects" on other chemical parameters (e.g., availability of Al, Fe, Mn, Zn, and Cu) and plant growth, but these indirect effects on the microbial communities are rarel...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0482-8
更新日期:2018-06-11 00:00:00
abstract:BACKGROUND:Antimicrobial resistance (AMR) is a major threat to public health. Microorganisms equipped with AMR genes are suggested to have partially emerged from natural habitats; however, this hypothesis remains inconclusive so far. To understand the consequences of the introduction of exogenic antimicrobials into nat...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00982-y
更新日期:2021-01-27 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0621-x
更新日期:2019-01-18 00:00:00
abstract:BACKGROUND:Periodontitis is an infectious and inflammatory disease of polymicrobial etiology that can lead to the destruction of bones and tissues that support the teeth. The management of chronic periodontitis (CP) relies heavily on elimination or at least control of known pathogenic consortia associated with the dise...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-32
更新日期:2014-08-26 00:00:00
abstract:BACKGROUND:Bacterial predation is an important selective force in microbial community structure and dynamics. However, only a limited number of predatory bacteria have been reported, and their predatory strategies and evolutionary adaptations remain elusive. We recently isolated a novel group of bacterial predators, Br...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00902-0
更新日期:2020-08-31 00:00:00
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 ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0679-5
更新日期:2019-04-25 00:00:00
abstract:BACKGROUND:Dental plaque is composed of hundreds of bacterial taxonomic units and represents one of the most diverse and stable microbial ecosystems associated with the human body. Taxonomic composition and functional capacity of mature plaque is gradually shaped during several stages of community assembly via processe...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0591-4
更新日期:2018-12-06 00:00:00
abstract:BACKGROUND:Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic co...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0255-9
更新日期:2017-04-08 00:00:00
abstract:BACKGROUND:Wastewater treatment plants (WWTPs) are recognized as hotspots for horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs). Despite our understanding of the composition and distribution of ARGs in WWTPs, the genetic location, host, and fate of ARGs remain largely unknown. RESULTS:In this study,...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0663-0
更新日期:2019-03-21 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0590-5
更新日期:2018-11-27 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00951-5
更新日期:2021-01-04 00:00:00
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 ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0635-4
更新日期:2019-02-11 00:00:00
abstract::An amendment to this paper has been published and can be accessed via the original article. ...
journal_title:Microbiome
pub_type: 已发布勘误
doi:10.1186/s40168-020-00905-x
更新日期:2020-08-20 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0770-y
更新日期:2019-12-02 00:00:00
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 ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0577-2
更新日期:2018-11-05 00:00:00
abstract:BACKGROUND:The human gut microbiome performs important functions in human health and disease. A classic example for host-gut microbial co-metabolism is host biosynthesis of primary bile acids and their subsequent deconjugation and transformation by the gut microbiome. To understand these system-level host-microbe inter...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0689-3
更新日期:2019-05-15 00:00:00
abstract:BACKGROUND:The correct establishment of the human gut microbiota represents a crucial development that commences at birth. Different hypotheses propose that the infant gut microbiota is derived from, among other sources, the mother's fecal/vaginal microbiota and human milk. RESULTS:The composition of bifidobacterial c...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0282-6
更新日期:2017-06-26 00:00:00
abstract:BACKGROUND:Determining the role of fomites in the transmission of SARS-CoV-2 is essential in the hospital setting and will likely be important outside of medical facilities as governments around the world make plans to ease COVID-19 public health restrictions and attempt to safely reopen economies. Expanding COVID-19 t...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00960-4
更新日期:2021-01-22 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0270-x
更新日期:2017-05-04 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0322-2
更新日期:2017-08-23 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-019-0760-0
更新日期:2019-11-06 00:00:00
abstract:BACKGROUND:Wheat residues are a crucial determinant of the epidemiology of Septoria tritici blotch, as they support the sexual reproduction of the causal agent Zymoseptoria tritici. We aimed to characterize the effect of infection with this fungal pathogen on the microbial communities present on wheat residues and to i...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0736-0
更新日期:2019-08-30 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0649-y
更新日期:2019-03-04 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0572-7
更新日期:2018-10-18 00:00:00
abstract:BACKGROUND:The role of the gut microbiome in arresting pathogen colonization and growth is important for protection against Clostridium difficile infection (CDI). Observational studies associate proton pump inhibitor (PPI) use and CDI incidence. We hypothesized that PPI use affected the distal gut microbiome over time,...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-42
更新日期:2014-11-25 00:00:00
abstract:BACKGROUND:Microbiome sequencing projects typically collect tens of millions of short reads per sample. Depending on the goals of the project, the short reads can either be subjected to direct sequence analysis or be assembled into longer contigs. The assembly of whole genomes from metagenomic sequencing reads is a ver...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0233-2
更新日期:2017-01-25 00:00:00
abstract:BACKGROUND:Polycyclic aromatic hydrocarbons (PAHs) are of environmental and public health concerns and contribute to adverse skin attributes such as premature skin aging and pigmentary disorder. However, little information is available on the potential roles of chronic urban PAH pollutant exposure on the cutaneous micr...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00874-1
更新日期:2020-06-26 00:00:00
abstract::The human microbiome refers to the genetic composition of microorganisms in a particular location in the human body. Emerging evidence over the past many years suggests that the microbiome constitute drivers of human fate almost at par with our genome and epigenome. It is now well accepted after decades of disbelief t...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00968-w
更新日期:2021-01-12 00:00:00