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 alternative to antibiotic growth promoters. Altered intestinal microbiota play important roles in growth promotion, but the underlying mechanism remains unknown. RESULTS:We generated 1.64 terabases of metagenomic data from 495 chicken intestinal digesta samples and constructed a comprehensive chicken gut microbial gene catalog (9.04 million genes), which is also the first gene catalog of an animal's gut microbiome that covers all intestinal compartments. Then, we identified the distinctive characteristics and temporal changes in the foregut and hindgut microbiota. Next, we assessed the impact of MCE on chickens and gut microbiota. Chickens fed with MCE had improved growth performance, and major microbial changes were confined to the foregut, with the predominant role of Lactobacillus being enhanced, and the amino acids, vitamins, and secondary bile acids biosynthesis pathways being upregulated, but lacked the accumulation of antibiotic-resistance genes. In comparison, treatment with chlortetracycline similarly enriched some biosynthesis pathways of nutrients in the foregut microbiota, but elicited an increase in antibiotic-producing bacteria and antibiotic-resistance genes. CONCLUSION:The reference gene catalog of the chicken gut microbiome is an important supplement to animal gut metagenomes. Metagenomic analysis provides insights into the growth-promoting mechanism of MCE, and underscored the importance of utilizing safe and effective growth promoters.
journal_name
Microbiomejournal_title
Microbiomeauthors
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 Jdoi
10.1186/s40168-018-0590-5subject
Has Abstractpub_date
2018-11-27 00:00:00pages
211issue
1issn
2049-2618pii
10.1186/s40168-018-0590-5journal_volume
6pub_type
杂志文章相关文献
Microbiome文献大全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:BACKGROUND:The interconnectivities of built and natural environments can serve as conduits for the proliferation and dissemination of antibiotic resistance genes (ARGs). Several studies have compared the broad spectrum of ARGs (i.e., "resistomes") in various environmental compartments, but there is a need to identify u...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0735-1
更新日期:2019-08-29 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0441-4
更新日期:2018-04-03 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:Our understanding of gut microbiota has been limited primarily to findings from human and laboratory animals, but what shapes the gut microbiota in nature remains largely unknown. To fill this gap, we conducted a comprehensive study of gut microbiota of a well-studied North American red squirrel (Tamiasciuru...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0382-3
更新日期:2017-12-21 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: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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-020-00907-9
更新日期:2020-08-31 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::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...
journal_title:Microbiome
pub_type: 信件
doi:10.1186/s40168-020-00839-4
更新日期:2020-06-08 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0128-z
更新日期:2015-12-10 00:00:00
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 ...
journal_title:Microbiome
pub_type: 杂志文章,评审
doi:10.1186/s40168-016-0203-0
更新日期:2016-11-01 00:00:00
abstract:BACKGROUND:High-throughput bacterial 16S rRNA gene sequencing followed by clustering of short sequences into operational taxonomic units (OTUs) is widely used for microbiome profiling. However, clustering of short 16S rRNA gene reads into biologically meaningful OTUs is challenging, in part because nucleotide variation...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-015-0105-6
更新日期:2015-10-05 00:00:00
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 ...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0547-8
更新日期:2018-09-12 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: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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0170-5
更新日期:2016-06-16 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: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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0629-2
更新日期:2019-02-01 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: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: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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0373-4
更新日期:2017-11-25 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-016-0181-2
更新日期:2016-07-07 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: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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/2049-2618-2-11
更新日期:2014-04-07 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:Several biotic and abiotic factors have been reported to influence the proliferation of microbes, including Legionella pneumophila, in hot water premise plumbing systems, but their combined effects have not been systematically evaluated. Here, we utilize simulated household water heaters to examine the effec...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-017-0348-5
更新日期:2017-10-04 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0442-3
更新日期:2018-03-27 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0722-6
更新日期:2019-08-01 00:00:00
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...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-019-0674-x
更新日期:2019-04-13 00:00:00
abstract:BACKGROUND:The caecal microbiota plays a key role in chicken health and performance, influencing digestion and absorption of nutrients, and contributing to defence against colonisation by invading pathogens. Measures of productivity and resistance to pathogen colonisation are directly influenced by chicken genotype, bu...
journal_title:Microbiome
pub_type: 杂志文章
doi:10.1186/s40168-018-0501-9
更新日期:2018-06-23 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