Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

Rajilić‐Stojanović, Mirjana; Maathuis, Annet; Heilig, Hans G.H.J.; Venema, Koen; Vos, Willem M. de; Smidt, Hauke

doi:10.1099/mic.0.042044-0

Cited by 83 publications

(72 citation statements)

References 56 publications

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“…4B). Bacteroides-dominated communities have been observed in several different in vitro bioreactor models (22,(51)(52)(53), which often use media of similar compositions for cultivation. Several parameters can affect the compositions of the microbial communities that are established in fecal bioreactors, including the source of fecal material and how it is processed, the medium composition and turnover time used for cultivation, and the availability of surfaces for biofilm formation (reviewed in reference 54).…”

Section: Discussionmentioning

confidence: 99%

Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates

et al. 2014

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Clostridium difficile infection is the most common cause of severe cases of antibiotic-associated diarrhea (AAD) and is a significant health burden. Recent increases in the rate of C. difficile infection have paralleled the emergence of a specific phylogenetic clade of C. difficile strains (ribotype 027; North American pulsed-field electrophoresis 1 [NAP1]; restriction endonuclease analysis [REA] group BI). Initial reports indicated that ribotype 027 strains were associated with increased morbidity and mortality and might be hypervirulent. Although subsequent work has raised some doubt as to whether ribotype 027 strains are hypervirulent, the strains are considered epidemic isolates that have caused severe outbreaks across the globe. We hypothesized that one factor that could lead to the increased prevalence of ribotype 027 strains would be if these strains had increased competitive fitness compared to strains of other ribotypes. We developed a moderate-throughput in vitro model of C. difficile infection and used it to test competition between four ribotype 027 clinical isolates and clinical isolates of four other ribotypes (001, 002, 014, and 053). We found that ribotype 027 strains outcompeted the strains of other ribotypes. A similar competitive advantage was observed when two ribotype pairs were competed in a mouse model of C. difficile infection. Based upon these results, we conclude that one possible mechanism through which ribotype 027 strains have caused outbreaks worldwide is their increased ability to compete in the presence of a complex microbiota.

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Section: Discussionmentioning

confidence: 99%

Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates

et al. 2014

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“…The enrichment of Firmicutes over Bacteroidetes and Protebacteria in the mucosal M-SHIME environment and the fact that this contributes to higher butyrate levels in the in vitro model further indicate that the M-SHIME is a significantly improved simulation of the intestinal microbiota compared with conventional in vitro models. The latter models are indeed confronted with lower abundances of Firmicutes, especially butyrate-producing species belonging to the Clostridium cluster XIVa and IV (Rajilić-Stojanović et al, 2010;Van den Abbeele et al, 2010), whereas Bacteroidetes and Proteobacteria are very abundant (Allison et al, 1989;Macfarlane et al, 1998;Mäkeläinen et al, 2009;Rajilić-Stojanović et al, 2010;Van den Abbeele et al, 2010), typically resulting in lower butyrate levels (Allison et al, 1989;Van den Abbeele et al, 2010). By avoiding washout of mucosal microbes, the M-SHIME allows mechanistic studies that not only focus on planktonic but also on surface-attached microbes, increasing the relevance of in vitro research.…”

Section: Discussionmentioning

confidence: 99%

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

et al. 2012

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The human gut is colonized by a complex microbiota with multiple benefits. Although the surfaceattached, mucosal microbiota has a unique composition and potential to influence human health, it remains difficult to study in vivo. Therefore, we performed an in-depth microbial characterization (human intestinal tract chip (HITChip)) of a recently developed dynamic in vitro gut model, which simulates both luminal and mucosal gut microbes (mucosal-simulator of human intestinal microbial ecosystem (M-SHIME)). Inter-individual differences among human subjects were confirmed and microbial patterns unique for each individual were preserved in vitro. Furthermore, in correspondence with in vivo studies, Bacteroidetes and Proteobacteria were enriched in the luminal content while Firmicutes rather colonized the mucin layer, with Clostridium cluster XIVa accounting for almost 60% of the mucin-adhered microbiota. Of the many acetate and/or lactate-converting butyrate producers within this cluster, Roseburia intestinalis and Eubacterium rectale most specifically colonized mucins. These 16S rRNA gene-based results were confirmed at a functional level as butyryl-CoA:acetate-CoA transferase gene sequences belonged to different species in the luminal as opposed to the mucin-adhered microbiota, with Roseburia species governing the mucosal butyrate production. Correspondingly, the simulated mucosal environment induced a shift from acetate towards butyrate. As not only inter-individual differences were preserved but also because compared with conventional models, washout of relevant mucin-adhered microbes was avoided, simulating the mucosal gut microbiota represents a breakthrough in modeling and mechanistically studying the human intestinal microbiome in health and disease. Finally, as mucosal butyrate producers produce butyrate close to the epithelium, they may enhance butyrate bioavailability, which could be useful in treating diseases, such as inflammatory bowel disease.

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“…Carcinomas and melanomas will be typed and sub-typed and the prognosis and treatment will be suggested. Using similar types of microarrays, skin microbiome can be comprehensively characterized and harmful bacteria and fungi identified [54][55][56]. Human papilloma virus, if present, can be easily genotyped [57].…”

Section: Skinomics In Our Futurementioning

confidence: 99%

SKINOMICS: Transcriptional Profiling in Dermatology and Skin Biology

Blumenberg¹

2015

Encyclopedia of Metagenomics

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Recent years witnessed the birth of bioinformatics technologies, which greatly advanced biological research. These 'omics' technologies address comprehensively the entire genome, transcriptome, proteome, microbiome etc. A large impetus in development of bioinformatics was the introduction of DNA microarrays for transcriptional profiling. Because of its accessibility, skin was among the first organs analyzed using DNA microarrays, and dermatology among the first medical disciplines to embrace the approach. Here, DNA microarray methodologies and their application in dermatology and skin biology are reviewed. The most studied disease has been, unsurprisingly, melanoma; markers of melanoma progression, metastatic potential and even melanoma markers in blood have been detected. The basal and squamous cell carcinomas have also been intensely studied. Psoriasis has been comprehensively explored using DNA microarrays, transcriptional changes correlated with genomic markers and several signaling pathways important in psoriasis have been identified. Atopic dermatitis, wound healing, keloids etc. have been analyzed using microarrays. Noninvasive skin sampling for microarray studies has been developed. Simultaneously, epidermal keratinocytes have been the subject of many skin biology studies because they respond to a rich variety of inflammatory and immunomodulating cytokines, hormones, vitamins, UV light, toxins and physical injury. The transcriptional changes occurring during epidermal differentiation and cornification have been identified and characterized. Recent studies identified the genes specifically expressed in human epidermal stem cells. As dermatology advances toward personalized medicine, microarrays and related 'omics' techniques will be directly applicable to the personalized dermatology practice of the future.

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Evaluating the microbial diversity of an in vitro model of the human large intestine by phylogenetic microarray analysis

Cited by 83 publications

References 56 publications

Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates

Epidemic Clostridium difficile Strains Demonstrate Increased Competitive Fitness Compared to Nonepidemic Isolates

Butyrate-producing Clostridium cluster XIVa species specifically colonize mucins in an in vitro gut model

SKINOMICS: Transcriptional Profiling in Dermatology and Skin Biology

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