Eukaryote Culturomics of the Gut Reveals New Species

Gouba, Nina; Raoult, Didier; Drancourt, Michel

doi:10.1371/journal.pone.0106994

Cited by 78 publications

(50 citation statements)

References 35 publications

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“…Furthermore, a reduction in microbiome diversity has been associated with inflammatory skin disorders (41). Although many studies evaluating microbial communities have applied a genomic approach, culturomics is emerging as a robust technique for detailed microbial identification to the species level (19)(20)(21)(22)(23)(24)(25)(26). As demonstrated herein, this level of detail is especially important for the skin and nasal flora, where closely related Gram-positive species predominate.…”

Section: Discussionmentioning

confidence: 95%

“…While microbial culture has traditionally been regarded as insensitive for detecting a majority of the microbiota, molecular methods have informed augmented culture approaches, yielding enhanced recovery of these microorganisms (19)(20)(21)(22)(23)(24)(25)(26). Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) is a rapid and costeffective technique that utilizes proteomic profiling for organism identification (27).…”

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confidence: 99%

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Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Burnham

Hogan

Wallace

et al. 2016

Antimicrob Agents Chemother

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Topical antimicrobials are often employed for decolonization and infection prevention and may alter the endogenous microbiota of the skin. The objective of this study was to compare the microbial communities and levels of richness and diversity in community-dwelling subjects and intensive care unit (ICU) patients before and after the use of topical decolonization protocols. We enrolled 15 adults at risk for Staphylococcus aureus infection. Community subjects (n ‫؍‬ 8) underwent a 5-day decolonization protocol (twice daily intranasal mupirocin and daily dilute bleach-water baths), and ICU patients (n ‫؍‬ 7) received daily chlorhexidine baths. Swab samples were collected from 5 anatomic sites immediately before and again after decolonization. A variety of culture media and incubation environments were used to recover bacteria and fungi; isolates were identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry. Overall, 174 unique organisms were recovered. Unique communities of organisms were recovered from the community-dwelling and hospitalized cohorts. In the communitydwelling cohort, microbial richness and diversity did not differ significantly between collections across time points, although the number of body sites colonized with S. aureus decreased significantly over time (P ‫؍‬ 0.004). Within the hospitalized cohort, richness and diversity decreased over time compared to those for the enrollment sampling (from enrollment to final sampling, P ‫؍‬ 0.01 for both richness and diversity). Topical antimicrobials reduced the burden of S. aureus while preserving other components of the skin and nasal microbiota. N osocomial infections pose significant clinical and financial burdens to patients and health care systems (1, 2). Colonization with potential pathogens serves as an endogenous source of infection (e.g., central line-associated bloodstream infection with Staphylococcus aureus) (3). For hospitalized patients, particularly those in intensive care units (ICUs), decolonization with topical antimicrobials, including chlorhexidine and/or mupirocin, has been demonstrated to reduce the acquisition of antibiotic-resistant microorganisms and the incidence of hospital-acquired infections (4-6). While decolonization has traditionally been employed in health care settings, the emergence of methicillinresistant S. aureus (MRSA) in the community and the resultant epidemic of skin and soft tissue infections (SSTIs) have led to the extrapolation of decolonization to outpatients to prevent recurrent SSTIs (7-10). As these broad-spectrum therapies are not pathogen specific (e.g., for MRSA or Enterobacteriaceae), these agents may suppress or eliminate other organisms on the skin and nasal mucosa, thereby potentially disrupting the balance of the microbiota, an important component of host defense against pathogenic organisms (11, 12). Indeed, this dysbiosis has been demonstrated for the intestinal microbiota following administration of oral antibiotics (13,14).Culture-independent molecular meth...

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Section: Discussionmentioning

confidence: 95%

mentioning

confidence: 99%

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Burnham

Hogan

Wallace

et al. 2016

Antimicrob Agents Chemother

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“…refs. [41][42][43] ), xerophiles (Wallemia sebi and W. muriae), 44 wood decay fungi, 22,45,46 and other organisms whose growth and nutrition requirements preclude any lasting role in the mammalian GI tract.…”

Section: Categories Of Gut Fungimentioning

confidence: 99%

Fungi in the healthy human gastrointestinal tract

2016

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Many species of fungi have been detected in the healthy human gut; however, nearly half of all taxa reported have only been found in one sample or one study. Fungi capable of growing in and colonizing the gut are limited to a small number of species, mostly Candida yeasts and yeasts in the family Dipodascaceae (Galactomyces, Geotrichum, Saprochaete). Malassezia and the filamentous fungus Cladosporium are potential colonizers; more work is needed to clarify their role. Other commonly-detected fungi come from the diet or environment but either cannot or do not colonize (Penicillium and Debaryomyces species, which are common on fermented foods but cannot grow at human body temperature), while still others have dietary or environmental sources (Saccharomyces cerevisiae, a fermentation agent and sometime probiotic; Aspergillus species, ubiquitous molds) yet are likely to impact gut ecology. The gut mycobiome appears less stable than the bacterial microbiome, and is likely subject to environmental factors.

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“…In contrast, the ciliate species ( Balantidium coli, Stentor roeseli and Vorticella campanula ) (Fig. , Table ) have been reported in the human intestinal tract . Although the stramenopiles comprise various types of algae, diatoms and other organisms that have morphological features similar to fungi, the genus Blastocystis (Fig.…”

Section: The Taxonomy Of Human Gut Eukaryamentioning

confidence: 99%

Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods

Hamad

Raoult

Bittar

2015

Parasite Immunology

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Eukaryotes are an important component of the human gut, and their relationship with the human host varies from parasitic to commensal. Understanding the diversity of human intestinal eukaryotes has important significance for human health. In the past few decades, most of the multitudes of techniques that are involved in the diagnosis of the eukaryotic population in the human intestinal tract were confined to pathological and parasitological aspects that mainly rely on traditionally based methods. However, development of culture-independent molecular techniques comprised of direct DNA extraction from faeces followed by sequencing, offer new opportunities to estimate the occurrence of eukaryotes in the human gut by providing data on the entire eukaryotic community, particularly not-yet-cultured or fastidious organisms. Further broad surveys of the eukaryotic communities in the gut based on high throughput tools such as next generation sequencing might lead to uncovering the real diversity of these ubiquitous organisms in the human intestinal tract and discovering the unrecognized roles of these eukaryotes in modulating the host immune system and inducing changes in host gut physiology and ecosystem.

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Eukaryote Culturomics of the Gut Reveals New Species

Cited by 78 publications

References 35 publications

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Topical Decolonization Does Not Eradicate the Skin Microbiota of Community-Dwelling or Hospitalized Adults

Fungi in the healthy human gastrointestinal tract

Repertory of eukaryotes (eukaryome) in the human gastrointestinal tract: taxonomy and detection methods

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