A comprehensive repertoire of prokaryotic species identified in human beings

Hugon, Perrine; Dufour, Jean-Charles; Colson, Philippe; Fournier, Pierre‐Edouard; Sallah, Kankoé; Raoult, Didier

doi:10.1016/s1473-3099(15)00293-5

Cited by 288 publications

(202 citation statements)

References 101 publications

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“…We used our own online prokaryotic repertoire 13 (http://hpr.mediterranee-infection.com/arkotheque/client/ ihu_bacteries/recherche/index.php) to classify all isolated prokaryotes into four categories: new prokaryote species, previously known prokaryote species in the human gut, known species from the environment but first isolated in humans, and known species from humans but first isolated in the human gut. Briefly, to complete the recent work identifying all the prokaryotes isolated in humans 13 , we examined methods by conducting a literature search, which included PubMed and books on infectious diseases. We examined the Medical Subject Headings (MeSH) indexing provided by Medline for bacteria isolated from the human gut and we then established two different queries to automatically obtain all articles indexed by Medline dealing with human gut isolation sites.…”

Section: Methodsmentioning

confidence: 99%

“…Moreover, the exploration of relations between the microbiota and human health require-both for an experimental model and therapeutic strategies-the growing of microorganisms in pure culture 10 , as recently demonstrated in elucidations of the role of Clostridium butyricum in necrotizing enterocolitis and the influence of gut microbiota on cancer immunotherapy effects 11,12 . In recent years, microbial culture techniques have been neglected, which explains why the known microbial community of the human gut is extremely low 13 . Before we initiated microbial culturomics 13 of the approximately 13,410 known bacterial and archaea species, 2,152 had been identified in humans and 688 bacteria and 2 archaea had been identified in the human gut.…”

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confidence: 99%

“…In recent years, microbial culture techniques have been neglected, which explains why the known microbial community of the human gut is extremely low 13 . Before we initiated microbial culturomics 13 of the approximately 13,410 known bacterial and archaea species, 2,152 had been identified in humans and 688 bacteria and 2 archaea had been identified in the human gut. Culturomics consists of the application of high-throughput culture conditions to the study of the human microbiota and uses matrix-assisted laser desorption/ ionization-time of flight (MALDI-TOF) or 16S rRNA amplification and sequencing for the identification of growing colonies, some of which have been previously unidentified 2 .…”

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confidence: 99%

“…We applied these 70 culture conditions (Supplementary Table 2a) to the study of 12 stool samples (Supplementary Table 1). Thanks to the implementation of the recently published repertoire of human bacteria 13 (see Methods), we determined that the isolated bacteria included 46 bacteria known from the gut but not recovered by culturomics before this work (new for culturomics), 38 that had already been isolated in humans but not from the gut (non-gut bacteria), 29 that had been isolated in humans for the first time (non-human bacteria) and 10 that were completely new species (unknown bacteria) ( Fig. 1 and Supplementary Tables 4a and 5).…”

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confidence: 99%

“…Among the gut species mentioned in the literature 13 and not previously recovered by culturomics, several were extremely oxygensensitive anaerobes, several were microaerophilic and several were Proteobacteria, and we focused on these bacteria (Supplementary Table 3). Because delay and storage may be critical with anaerobes, we inoculated 28 stools immediately upon collection.…”

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RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

et al. 2016

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Metagenomics revolutionized the understanding of the relations among the human microbiome, health and diseases, but generated a countless number of sequences that have not been assigned to a known microorganism 1 . The pure culture of prokaryotes, neglected in recent decades, remains essential to elucidating the role of these organisms 2 . We recently introduced microbial culturomics, a culturing approach that uses multiple culture conditions and matrix-assisted laser desorption/ionization-time of flight and 16S rRNA for identification 2 . Here, we have selected the best culture conditions to increase the number of studied samples and have applied new protocols (fresh-sample inoculation; detection of microcolonies and specific cultures of Proteobacteria and microaerophilic and halophilic prokaryotes) to address the weaknesses of the previous studies 3-5 . We identified 1,057 prokaryotic species, thereby adding 531 species to the human gut repertoire: 146 bacteria known in humans but not in the gut, 187 bacteria and 1 archaea not previously isolated in humans, and 197 potentially new species. Genome sequencing was performed on the new species. By comparing the results of the metagenomic and culturomic analyses, we show that the use of culturomics allows the culture of organisms corresponding to sequences previously not assigned. Altogether, culturomics doubles the number of species isolated at least once from the human gut.

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Section: Methodsmentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

et al. 2016

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Guidelines for the Prevention, Diagnosis, and Management of Urinary Tract Infections in Pediatrics and Adults

Nelson,

Tarık Aslan,

Beahm

et al. 2024

JAMA Netw Open

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ImportanceTraditional approaches to practice guidelines frequently result in dissociation between strength of recommendation and quality of evidence.ObjectiveTo create a clinical guideline for the diagnosis and management of urinary tract infections that addresses the gap between the evidence and recommendation strength.Evidence ReviewThis consensus statement and systematic review applied an approach previously established by the WikiGuidelines Group to construct collaborative clinical guidelines. In May 2023, new and existing members were solicited for questions on urinary tract infection prevention, diagnosis, and management. For each topic, literature searches were conducted up until early 2024 in any language. Evidence was reported according to the WikiGuidelines charter: clear recommendations were established only when reproducible, prospective, controlled studies provided hypothesis-confirming evidence. In the absence of such data, clinical reviews were developed discussing the available literature and associated risks and benefits of various approaches.FindingsA total of 54 members representing 12 countries reviewed 914 articles and submitted information relevant to 5 sections: prophylaxis and prevention (7 questions), diagnosis and diagnostic stewardship (7 questions), empirical treatment (3 questions), definitive treatment and antimicrobial stewardship (10 questions), and special populations and genitourinary syndromes (10 questions). Of 37 unique questions, a clear recommendation could be provided for 6 questions. In 3 of the remaining questions, a clear recommendation could only be provided for certain aspects of the question. Clinical reviews were generated for the remaining questions and aspects of questions not meeting criteria for a clear recommendation.Conclusions and RelevanceIn this consensus statement that applied the WikiGuidelines method for clinical guideline development, the majority of topics relating to prevention, diagnosis, and treatment of urinary tract infections lack high-quality prospective data and clear recommendations could not be made. Randomized clinical trials are underway to address some of these gaps; however further research is of utmost importance to inform true evidence-based, rather than eminence-based practice.

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The link between gut microbiome and Alzheimer's disease: From the perspective of new revised criteria for diagnosis and staging of Alzheimer's disease

Liang,

Liu,

Cheng

et al. 2024

Alzheimer's & Dementia

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Over the past decades, accumulating evidence suggests that the gut microbiome exerts a key role in Alzheimer's disease (AD). The Alzheimer's Association Workgroup is updating the diagnostic criteria for AD, which changed the profiles and categorization of biomarkers from “AT(N)” to “ATNIVS.” Previously, most of studies focus on the correlation between the gut microbiome and amyloid beta deposition (“A”), the initial AD pathological feature triggering the “downstream” tauopathy and neurodegeneration. However, limited research investigated the interactions between the gut microbiome and other AD pathogenesis (“TNIVS”). In this review, we summarize current findings of the gut microbial characteristics in the whole spectrum of AD. Then, we describe the association of the gut microbiome with updated biomarker categories of AD pathogenesis. In addition, we outline the gut microbiome‐related therapeutic strategies for AD. Finally, we discuss current key issues of the gut microbiome research in the AD field and future research directions.Highlights The new revised criteria for Alzheimer's disease (AD) proposed by the Alzheimer's Association Workgroup have updated the profiles and categorization of biomarkers from “AT(N)” to “ATNIVS.” The associations of the gut microbiome with updated biomarker categories of AD pathogenesis are described. Current findings of the gut microbial characteristics in the whole spectrum of AD are summarized. Therapeutic strategies for AD based on the gut microbiome are proposed.

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A comprehensive repertoire of prokaryotic species identified in human beings

Cited by 288 publications

References 101 publications

RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics

Guidelines for the Prevention, Diagnosis, and Management of Urinary Tract Infections in Pediatrics and Adults

The link between gut microbiome and Alzheimer's disease: From the perspective of new revised criteria for diagnosis and staging of Alzheimer's disease

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