Abstract:
:Dysbiosis of the gut microbiome, including elevated abundance of putative leading bacterial triggers such as E. coli in inflammatory bowel disease (IBD) patients, is of great interest. To date, most E. coli studies in IBD patients are focused on clinical isolates, overlooking their relative abundances and turnover over time. Metagenomics-based studies, on the other hand, are less focused on strain-level investigations. Here, using recently developed bioinformatic tools, we analyzed the abundance and properties of specific E. coli strains in a Crohns disease (CD) patient longitudinally, while also considering the composition of the entire community over time. In this report, we conducted a pilot study on metagenomic-based, strain-level analysis of a time-series of E. coli strains in a left-sided CD patient, who exhibited sustained levels of E. coli greater than 100X healthy controls. We: (1) mapped out the composition of the gut microbiome over time, particularly the presence of E. coli strains, and found that the abundance and dominance of specific E. coli strains in the community varied over time; (2) performed strain-level de novo assemblies of seven dominant E. coli strains, and illustrated disparity between these strains in both phylogenetic origin and genomic content; (3) observed that strain ST1 (recovered during peak inflammation) is highly similar to known pathogenic AIEC strains NC101 and LF82 in both virulence factors and metabolic functions, while other strains (ST2-ST7) that were collected during more stable states displayed diverse characteristics; (4) isolated, sequenced, experimentally characterized ST1, and confirmed the accuracy of the de novo assembly; and (5) assessed growth capability of ST1 with a newly reconstructed genome-scale metabolic model of the strain, and showed its potential to use substrates found abundantly in the human gut to outcompete other microbes. In conclusion, inflammation status (assessed by the blood C-reactive protein and stool calprotectin) is likely correlated with the abundance of a subgroup of E. coli strains with specific traits. Therefore, strain-level time-series analysis of dominant E. coli strains in a CD patient is highly informative, and motivates a study of a larger cohort of IBD patients.
journal_name
Front Microbioljournal_title
Frontiers in microbiologyauthors
Fang X,Monk JM,Nurk S,Akseshina M,Zhu Q,Gemmell C,Gianetto-Hill C,Leung N,Szubin R,Sanders J,Beck PL,Li W,Sandborn WJ,Gray-Owen SD,Knight R,Allen-Vercoe E,Palsson BO,Smarr Ldoi
10.3389/fmicb.2018.02559subject
Has Abstractpub_date
2018-10-30 00:00:00pages
2559issn
1664-302Xjournal_volume
9pub_type
杂志文章abstract::Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. As reported in other countries, after the rise and fall of the pandemic strain in Chile, other post-pandemic strains have been associated with clinical cases, including strains lacking the major toxins TDH and TRH. Since the prese...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00161
更新日期:2018-02-08 00:00:00
abstract::Porcine circovirus-like virus P1 is an important pathogen of the current pig industry, the infection mechanism is not entirely clear. Wnt signaling pathway plays an important role in the growth of young animals and infection of some viruses. This study was designed to demonstrate the effects of P1 infection on the Wnt...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00390
更新日期:2018-03-12 00:00:00
abstract::Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) compete for nitrate in natural and engineered environments. A known important factor in this microbial competition is the ratio of available electron donor and elector acceptor, here expressed as Ac/N ratio (acetate/nitrate-nitrogen). We studied th...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01842
更新日期:2016-11-24 00:00:00
abstract::IncI-complex plasmids can be divided into seven subgroups IncI1, IncI2, IncIγ, IncB/O, IncK1, IncK2, and IncZ. In this study, a replicon-based scheme was proposed for typing IncI-complex plasmids into four separately clustering subgroups IncI2, IncI1/B/O, IncIγ/K1 and IncK2/Z, the last three of which were combined fro...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.00048
更新日期:2019-01-29 00:00:00
abstract::Biofilms, which are complex microbial communities embedded in the protective extracellular polymeric substances (EPS), are difficult to remove in food production facilities. In this study, the use of acidic electrolyzed water (AEW) to remove foodborne pathogen biofilms was evaluated. We used a green fluorescent protei...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.00988
更新日期:2017-06-07 00:00:00
abstract::Several previous studies have shown that bacteriophages can significantly affect the production of various cytokines. The aim of this present study was to investigate the inflammatory effects and mechanisms of bacteriophage vB_SauM_JS25 in stimulated MAC-T bovine mammary epithelial cells by real-time polymerase chain ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.01614
更新日期:2018-07-23 00:00:00
abstract::The human enteric pathogen Salmonella enterica leads a cross-kingdom lifestyle, actively colonizing and persisting on plants in between animal hosts. One of the questions that arises from this dual lifestyle is how S. enterica is able to adapt to such divergent hosts. Metabolic pathways required for S. enterica animal...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00695
更新日期:2018-05-08 00:00:00
abstract::Sewage waste represents an ecosystem of complex and interactive microbial consortia which proliferate with different kinetics according to their individual genetic as well as metabolic potential. We performed metagenomic shotgun sequencing on Ion-Torrent platform, to explore the microbial community structure, their bi...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01382
更新日期:2017-07-19 00:00:00
abstract::Based on the Stable Ecotype Model, evolution leads to the divergence of ecologically distinct populations (e.g., with different niches and/or behaviors) of ecologically interchangeable membership. In this study, pyrosequencing was used to provide deep sequence coverage of Synechococcus psaA genes and transcripts over ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.00590
更新日期:2015-06-22 00:00:00
abstract::Introduction:Aspergillus can cause different allergic diseases including allergic bronchopulmonary aspergillosis (ABPA) and allergic fungal rhinosinusitis (AFRS). ABPA is allergic pulmonary disease against Aspergillus antigens. AFRS is a type of chronic rhinosinusitis (CRS) presented as hypersensitivity reactions to t...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00583
更新日期:2018-04-03 00:00:00
abstract::Myocyanophages, a group of viruses infecting cyanobacteria, are abundant and play important roles in elemental cycling. Here we investigated the particle-associated viral communities retained on 0.2 μm filters and in sediment samples (representing ancient cyanophage communities) from four ocean and three lake location...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00887
更新日期:2018-05-03 00:00:00
abstract::Desulfotomaculum reducens strain MI-1 is a Gram-positive, sulfate-reducing bacterium also capable of reducing Fe(III). Metal reduction in Gram-positive bacteria is poorly understood. Here, we investigated Fe(III) reduction with lactate, a non-fermentable substrate, as the electron donor. Lactate consumption is concomi...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2014.00432
更新日期:2014-08-19 00:00:00
abstract::Kaposi sarcoma herpesvirus (KSHV) is the etiologic agent of Kaposi sarcoma (KS) and certain rare B cell lymphoproliferative disorders. KSHV infection of endothelial cells (EC) in vitro increases expression of the inducible host-encoded enzyme heme oxygenase-1 (HO-1), which is also strongly expressed in KS tumors. HO-1...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.00568
更新日期:2017-04-03 00:00:00
abstract::Acinetobacter baumannii is emerging as a challenging nosocomial pathogen due to its rapid evolution of antibiotic resistance. We report characterization of two novel bacteriophages, PBAB08 and PBAB25, infecting clinically isolated, multidrug-resistant (MDR) A. baumannii strains. Both phages belonged to Myoviridae of C...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00696
更新日期:2018-04-10 00:00:00
abstract::Microbiome research has increased dramatically in recent years, driven by advances in technology and significant reductions in the cost of analysis. Such research has unlocked a wealth of data, which has yielded tremendous insight into the nature of the microbial communities, including their interactions and effects, ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.00136
更新日期:2020-02-19 00:00:00
abstract::In many caries-promoting Streptococcus species, glucosyltransferases (Gtfs) are recognized as key enzymes contributing to the modification of biofilm structures, disruption of homeostasis of healthy microbiota community and induction of caries development. It is therefore of great interest to investigate how Gtf genes...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.02979
更新日期:2018-12-04 00:00:00
abstract::Pseudomonas aeruginosa is an opportunistic pathogen commonly infecting immunocompromised patients with diseases like cystic fibrosis (CF) and cancers and has high rates of recurrence and mortality. The treatment efficacy can be significantly worsened by the multidrug resistance (MDR) of P. aeruginosa, and there is inc...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.01423
更新日期:2020-07-08 00:00:00
abstract::Nitrile hydratases have received significant interest both in the large-scale industrial production of acrylamide and nicotinamide, and the remediation of environmental contamination with nitrile-containing pollutants. Almost all known nitrile hydratases include an α-subunit (AnhA) and β-subunit (AnhB), and a specific...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.01419
更新日期:2020-06-25 00:00:00
abstract::The changes of gastric microbiome across stages of neoplastic progression remain poorly understood, especially for intraepithelial neoplasia (IN) which has been recognized as a phenotypic bridge between atrophic/intestinal metaplastic lesions and invasive cancer. The gastric microbiota was investigated in 30 healthy c...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2020.00997
更新日期:2020-05-29 00:00:00
abstract::Synechococcus elongatus PCC 7942 is a paradigmatic model organism for nitrogen regulation in cyanobacteria. Expression of genes involved in nitrogen assimilation is positively regulated by the 2-oxoglutarate receptor and global transcriptional regulator NtcA. Maximal activation requires the subsequent binding of the c...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01244
更新日期:2017-07-11 00:00:00
abstract::The present study aimed to understand the biofilm formation mechanism of Propionibacterium acnes by analyzing the components and structure of the biofilms. P. acnes strains were isolated from the surface of explanted cardiac pacemaker devices that exhibited no clinical signs of infection. Culture tests using a simple ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2018.00182
更新日期:2018-02-14 00:00:00
abstract::In this study we report the effects of fungal metabolites isolated from cultures of the fungus Trichoderma citrinoviride ITEM 4484 on the feeding preference of the aphid Rhopalosiphum padi, a major pest of cereal crops. Different phagodeterrent metabolites were purified by a combination of direct and reverse phase col...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.00297
更新日期:2016-03-10 00:00:00
abstract::The rumen contains a multi-kingdom, commensal microbiome, including protozoa, bacteria, archaea, fungi and viruses, which enables ruminant herbivores to ferment and utilize plant feedstuffs that would be otherwise indigestible. Within the rumen, virus populations are diverse and highly abundant, often out-numbering th...
journal_title:Frontiers in microbiology
pub_type: 杂志文章,评审
doi:10.3389/fmicb.2020.00450
更新日期:2020-03-26 00:00:00
abstract::Isolated elongate spore-like cells present in the >1600 Ma-old Salkhan Limestone of the Semri Group, Vindhayan Supergroup, India are considered akinetes of the heterocystous cyanobacteria. Small to large size, and young (single walled) to mature (double walled) akinetes - namely, Archaeoellipsoides bactroformis, A. co...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2019.00397
更新日期:2019-03-12 00:00:00
abstract::In Liberibacter asiaticus, PrbP is an important transcriptional accessory protein that was found to regulate gene expression through interactions with the RNA polymerase β-subunit and a specific sequence on the promoter region. It was found that inactivation of PrbP, using the inhibitor tolfenamic acid, resulted in a ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.01591
更新日期:2017-08-23 00:00:00
abstract::Polymerase basic protein 1 (PB1), the catalytic core of the influenza A virus RNA polymerase complex, is essential for viral transcription and replication. Dendritic cells (DCs) possess important antigen presenting ability and a crucial role in recognizing and clearing virus. MicroRNA (miRNA) influence the development...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.00287
更新日期:2017-03-22 00:00:00
abstract::Acidithiobacillus caldus is an extremely acidophilic sulfur-oxidizer with specialized characteristics, such as tolerance to low pH and heavy metal resistance. To gain novel insights into its genetic complexity, we chosen six A. caldus strains for comparative survey. All strains analyzed in this study differ in geograp...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01960
更新日期:2016-12-06 00:00:00
abstract::Marine Synechococcus has successfully adapted to environments with different light colors, which likely contributes to this genus being the second most abundant group of microorganisms worldwide. Populations of Synechococcus that grow in deep, blue ocean waters contain large amounts of the blue-light absorbing chromop...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2017.00243
更新日期:2017-02-21 00:00:00
abstract::In smallholder farms of Côte d'Ivoire, particularly in the northeast of the country, Cajanus cajan (pigeonpea) has become an important crop because of its multiple beneficial facets. Pigeonpea seeds provide food to make ends meet, are sold on local markets, and aerial parts serve as forage for animals. Since it fixes ...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2016.01793
更新日期:2016-11-11 00:00:00
abstract::Phosphatidylglycerol (PG) is an indispensable phospholipid class with photosynthetic function in plants and cyanobacteria. However, its biosynthesis in eukaryotic green microalgae is poorly studied. Here, we report the isolation and characterization of two homologs (CrPGP1 and CrPGP2) of phosphatidylglycerophosphate s...
journal_title:Frontiers in microbiology
pub_type: 杂志文章
doi:10.3389/fmicb.2015.00842
更新日期:2015-08-24 00:00:00