Cited by 236Gut microbiota and healthMicrobial Community Ecology and PhysiologyBacterial Identification and Susceptibility Testing

The DOI matches its Crossref record; 90 of the 90 references it cites were found in a registry or an index.

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

Open access

Bilen, Melhem, Dufour, Jean-Charles, Lagier, Jean-Christophe, Cadoret, Fréderic, Daoud, Ziad, Dubourg, Grégory, Raoult, Didier·2018·Microbiome

DOI 10.1186/s40168-018-0485-5PMC PMC5966928

Open this paper in CoChat — free account Open PDF

Abstract

After a decade of research and metagenomic analyses, our knowledge of the human microbiota appears to have reached a plateau despite promising results. In many studies, culture has proven to be essential in describing new prokaryotic species and filling metagenomic gaps. In 2015, only 2172 different prokaryotic species were reported to have been isolated at least once from the human body as pathogens or commensals. In this review, we update the previous repertoire by reporting the different species isolated from the human body to date, increasing it by 28% to reach a total of 2776 species associated with human beings. They have been classified into 11 different phyla, mostly the Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. Finally, culturomics contributed up to 66.2% towards updating this repertoire by reporting 400 species, of which 288 were novel. This demonstrates the need to continue the culturing work, which seems essential in order to decipher the hidden human microbial content.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Integrity signals

Registry

Crossref · 10.1186/s40168-018-0485-5

Cites

90 of 90 references verified0 citation errors · 0 not checkable

Statistics

Fig. 1 All 2776 species isolated at least once from humans by culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the repertoireCC BY · PubMed Central

Fig. 2 Distribution of bacterial species reported in this repertoire according to their phylum, based on the NCBI taxonomy classification with the highest category being clustered in the Firmicutes phylum. Cyanobacteria, Deferribacteres, Spirochaetes, Synergistetes, and Tenericutes represent minority phyla in this repertoire, with 1, 1, 1, 3, 3, and 3 different species, respectivelyCC BY · PubMed Central

Fig. 3 All 2776 species isolated at least once from humans using culture. Using the online tool wordle (www.wordle.net), the size of the name of each species is proportional to the number of times it occurs in the database. In this image, only the species name was taken into consideration, excluding the genusCC BY · PubMed Central

Fig. 4 Distribution of bacterial species isolated from the gut using culturomics, according to the phylum to which they belong, based on the NCBI taxonomy classification, with the highest clustering in the Firmicutes phylumCC BY · PubMed Central

Fig. 5 Number of reported species isolated for the first time in humans by culturomics using the new species announcement format compared to the full description formatCC BY · PubMed Central

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

3 retracted

RETRACTED ARTICLE: Culture of previously uncultured members of the human gut microbiota by culturomics
Lagier, J.-C., Khelaifia, S., Alou, M. T., Ndongo, S., Dione, N., Hugon, P., Caputo, A., Cadoret, F., Traore, S. I., Seck, E. H., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.203 · Cited by 951
Self-citation
Retracted
RETRACTED ARTICLE: Increased Gut Redox and Depletion of Anaerobic and Methanogenic Prokaryotes in Severe Acute Malnutrition
Million, M., Alou, M. T., Khelaifia, S., Bachar, D., Lagier, J., Dione, N., Brah, S., Hugon, P., Lombard, V., Armougom, F., et al. (2016) · Scientific Reports · doi:10.1038/srep26051 · Cited by 204
Self-citation
Retracted
RETRACTED ARTICLE: Culturomics identified 11 new bacterial species from a single anorexia nervosa stool sample
Pfleiderer, A., Lagier, J., Armougom, F., Robert, C., Vialettes, B., & Raoult, D. (2013) · European Journal of Clinical Microbiology & Infectious Diseases · doi:10.1007/s10096-013-1900-2 · Cited by 158
Self-citation
Retracted
An obesity-associated gut microbiome with increased capacity for energy harvest
Turnbaugh, P. J., Ley, R. E., Mahowald, M. A., Magrini, V., Mardis, E. R., & Gordon, J. I. (2006) · Nature · doi:10.1038/nature05414 · Cited by 12,444
Structure, function and diversity of the healthy human microbiome
The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726
Human gut microbes associated with obesity
Ley, R. E., Turnbaugh, P. J., Klein, S., & Gordon, J. I. (2006) · Nature · doi:10.1038/4441022a · Cited by 8,785
Diversity of the Human Intestinal Microbial Flora
Eckburg, P. B., Bik, E. M., Bernstein, C. N., Purdom, E., Dethlefsen, L., Sargent, M., Gill, S. R., Nelson, K. E., & Relman, D. A. (2005) · Science · doi:10.1126/science.1110591 · Cited by 7,913
Obesity alters gut microbial ecology
Ley, R. E., Bäckhed, F., Turnbaugh, P., Lozupone, C. A., Knight, R. D., & Gordon, J. I. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504978102 · Cited by 6,176
The human microbiome project
Turnbaugh, P. J., Ley, R. E., Hamady, M., Fraser-Liggett, C. M., Knight, R., & Gordon, J. I. (2007) · Nature · doi:10.1038/nature06244 · Cited by 6,091
Gut microbiome influences efficacy of PD-1-based immunotherapy against epithelial tumors
Routy, B., Le Chatelier, E., Derosa, L., Duong, C. P. M., Alou, M. T., Daillère, R., Fluckiger, A., Messaoudene, M., Rauber, C., Roberti, M. P., et al. (2018) · Science · doi:10.1126/science.aan3706 · Cited by 5,671
Self-citation

Show all 90 references

Sorted by citations

The Microbiota-Gut-Brain Axis
Cryan, J. F., O'Riordan, K. J., Cowan, C. S. M., Sandhu, K. V., Bastiaanssen, T. F. S., Boehme, M., Codagnone, M. G., Cussotto, S., Fulling, C., Golubeva, A. V., et al. (2019) · Physiological Reviews · doi:10.1152/physrev.00018.2018 · Cited by 5,286
Sex differences in gut microbiota
Kim, Y. S., Unno, T., Kim, B.-Y., & Park, M.-S. (2020) · The World Journal of Men s Health · doi:10.5534/wjmh.190009 · Cited by 610
Gut Bacteria and Neurotransmitters
Dicks, L. M. T. (2022) · Microorganisms · doi:10.3390/microorganisms10091838 · Cited by 482
Nutritional Components in Western Diet Versus Mediterranean Diet at the Gut Microbiota–Immune System Interplay. Implications for Health and Disease
Montero, C. G., Fraile‐Μartinez, O., Gomez-Lahoz, A. M., Pekarek, L., Castellanos, A. J., Noguerales-Fraguas, F., Coca, S., Guijarro, L. G., García‐Honduvilla, N., Asúnsolo, Á., et al. (2021) · Nutrients · doi:10.3390/nu13020699 · Cited by 487
Next generation probiotics in disease amelioration
Chang, C., Lin, T., Tsai, Y., Wu, T.-R., Lai, W.-F., Lu, C., & Lai, H. (2019) · Journal of Food and Drug Analysis · doi:10.1016/j.jfda.2018.12.011 · Cited by 398
The impact of the Fungus-Host-Microbiota interplay uponCandida albicansinfections: current knowledge and new perspectives
d’Enfert, C., Kaune, A.-K., Alaban, L. R., Chakraborty, S., Cole, N. L., Delavy, M., Kosmala, D., Marsaux, B., Fróis-Martins, R., Morelli, M., et al. (2020) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuaa060 · Cited by 377
Exploring the emerging role of the microbiome in cancer immunotherapy
Fessler, J. L., Matson, V. Z., & Gajewski, T. F. (2019) · Journal for ImmunoTherapy of Cancer · doi:10.1186/s40425-019-0574-4 · Cited by 325
Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation
Liu, S., Moon, C. D., Zheng, N., Huws, S., Zhao, S., & Wang, J. (2022) · Microbiome · doi:10.1186/s40168-022-01272-5 · Cited by 278
Microbiota in Tumors: From Understanding to Application
Xie, Y., Xie, F., Zhou, X., Zhang, L., Yang, B., Huang, J., Wang, F., Yan, H., Zhang, L., Zhang, L., et al. (2022) · Advanced Science · doi:10.1002/advs.202200470 · Cited by 224
The microbiome of pest insects: it is not just bacteria
Gurung, K., Wertheim, B., & Salles, J. F. (2019) · Entomologia Experimentalis et Applicata · doi:10.1111/eea.12768 · Cited by 204
You’ve got male: Sex and the microbiota-gut-brain axis across the lifespan
Jaggar, M., Rea, K., Spichak, S., Dinan, T. G., & Cryan, J. F. (2020) · Frontiers in Neuroendocrinology · doi:10.1016/j.yfrne.2019.100815 · Cited by 200
Synthetic ecology of the human gut microbiota
Vrancken, G., Gregory, A., Huys, G. R. B., Faust, K., & Raes, J. (2019) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0264-8 · Cited by 196
Next-generation probiotics: the upcoming biotherapeutics
Al-Fakhrany, O. M., & Elekhnawy, E. (2024) · Molecular Biology Reports · doi:10.1007/s11033-024-09398-5 · Cited by 208
Pursuing Human-Relevant Gut Microbiota-Immune Interactions
Spencer, S. P., Fragiadakis, G. K., & Sonnenburg, J. L. (2019) · Immunity · doi:10.1016/j.immuni.2019.08.002 · Cited by 167
Vitamin D and the Host-Gut Microbiome: A Brief Overview
Akimbekov, N. S., Digel, I., Sherelkhan, D. K., Lutfor, A. B., & Razzaque, M. S. (2020) · ACTA HISTOCHEMICA ET CYTOCHEMICA · doi:10.1267/ahc.20011 · Cited by 153
Repertoire of Human Breast and Milk Microbiota: A Systematic Review
Togo, A. H., Dufour, J.-C., Lagier, J., Dubourg, G., Raoult, D., & Million, M. (2019) · Future Microbiology · doi:10.2217/fmb-2018-0317 · Cited by 148
Self-citation
Gut Microbiota: A Perspective for Psychiatrists
Rea, K., Dinan, T. G., & Cryan, J. F. (2019) · Neuropsychobiology · doi:10.1159/000504495 · Cited by 146
Pesticide exposure and the microbiota-gut-brain axis
Matsuzaki, R., Gunnigle, E., Geissen, V., Clarke, G. A., Nagpal, J. K., & Cryan, J. F. (2023) · The ISME Journal · doi:10.1038/s41396-023-01450-9 · Cited by 129
Integrated multi‐omics approaches to understand microbiome assembly in Jiuqu , a mixed‐culture starter
Kang, J., Xue, Y., Chen, X., & Han, B. (2022) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.13025 · Cited by 109
Gut Microbiota Interaction with the Central Nervous System throughout Life
Ojeda, J., Ávila, A., & Vidal, P. M. (2021) · Journal of Clinical Medicine · doi:10.3390/jcm10061299 · Cited by 112
Exhaustive repertoire of human vaginal microbiota
Diop, K., Dufour, J.-C., Levasseur, A., & Fenollar, F. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2018.11.002 · Cited by 103
Self-citation
The gut microbiota–brain axis in neurological disorders
You, M., Chen, N., Yang, Y., Cheng, L., He, H., Cai, Y., Liu, Y., Liu, H., & Hong, G. (2024) · MedComm · doi:10.1002/mco2.656 · Cited by 113
Role of prebiotics in enhancing the function of next-generation probiotics in gut microbiota
Fei, Y., Chen, Z., Han, S., Zhang, S., Zhang, T., Lu, Y., Berglund, B., Xiao, H., Li, L., & Yao, M. (2021) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2021.1958744 · Cited by 105
Next generation probiotics for human health: An emerging perspective
Jan, T., Negi, R., Sharma, B., Kumar, S., Singh, S., Rai, A. K., Shreaz, S., Rustagi, S., Chaudhary, N., Kaur, T., et al. (2024) · Heliyon · doi:10.1016/j.heliyon.2024.e35980 · Cited by 95
Optimization and standardization of the culturomics technique for human microbiome exploration
Diakite, A., Dubourg, G., Dione, N., Afouda, P., Bellali, S., Ngom, I. I., Valles, C., Tall, M. L., Lagier, J., & Raoult, D. (2020) · Scientific Reports · doi:10.1038/s41598-020-66738-8 · Cited by 95
Self-citation
Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus
Wu, L., Xie, X., Li, Y., Liang, T., Zhong, H., Yang, L., Yu, X., Zhang, J., Ding, Y., & Wu, Q. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00366-0 · Cited by 102
Shining Light on Human Gut Bacteriophages
Guerin, E., & Hill, C. (2020) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2020.00481 · Cited by 88
Unfolding the Human Milk Microbiome Landscape in the Omics Era
Ruíz, L., García-Carral, C., & Rodríguez, J. M. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01378 · Cited by 94
The Role of Gram-Negative Bacteria in Urinary Tract Infections: Current Concepts and Therapeutic Options
Behzadi, P., Urbán, E. Z., Matúz, M., Benkő, R., & Gajdács, M. (2020) · Advances in experimental medicine and biology · doi:10.1007/5584_2020_566 · Cited by 97
Culturomics and metagenomics: In understanding of environmental resistome
Nowrotek, M., Jałowiecki, Ł., Harnisz, M., & Płaza, G. A. (2019) · Frontiers of Environmental Science & Engineering · doi:10.1007/s11783-019-1121-8 · Cited by 81
RETRACTED: Among Live and Dead Bacteria, the Optimization of Sample Collection and Processing Remains Essential in Recovering Gut Microbiota Components
Bellali, S., Lagier, J., Raoult, D., & Khalil, J. Y. B. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.01606 · Cited by 73
Self-citation
Retracted
Characterization of Lung and Oral Microbiomes in Lung Cancer Patients Using Culturomics and 16S rRNA Gene Sequencing
Sun, Y., Liu, Y., Li, J., Tan, Y., An, T., Zhuo, M., Pan, Z., Ma, M., Jia, B., Zhang, H., et al. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.00314-23 · Cited by 77
Optimization of Culturomics Strategy in Human Fecal Samples
Chang, Y., Hou, F., Pan, Z., Huang, Z., Han, N., Bin, L., Deng, H., Li, Z., Ding, L., Gao, H., et al. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02891 · Cited by 69
A Meta-Analysis Approach to Defining the Culturable Core of Plant Endophytic Bacterial Communities
Riva, V., Mapelli, F., Bagnasco, A., Mengoni, A., & Borin, S. (2022) · Applied and Environmental Microbiology · doi:10.1128/aem.02537-21 · Cited by 70
RETRACTED: Deciphering the Urinary Microbiota Repertoire by Culturomics Reveals Mostly Anaerobic Bacteria From the Gut
Dubourg, G., Morand, A., Mekhalif, F., Godefroy, R., Corthier, A., Yacouba, A., Diakite, A., Cornu, F., Cresci, M., Brahimi, S., et al. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.513305 · Cited by 66
Self-citation
Retracted
Our Mental Health Is Determined by an Intrinsic Interplay between the Central Nervous System, Enteric Nerves, and Gut Microbiota
Dicks, L. M. T. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms25010038 · Cited by 74
How MALDI-TOF mass spectrometry can aid the diagnosis of hard-to-identify pathogenic bacteria – the rare and the unknown
Kostrzewa, M., Nagy, E., Schröttner, P., & Pranada, A. B. (2019) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2019.1643238 · Cited by 64
Extensive culturomics of 8 healthy samples enhances metagenomics efficiency
Diakite, A., Dubourg, G., Dione, N., Afouda, P., Bellali, S., Ngom, I. I., Valles, C., Million, M., Levasseur, A., Cadoret, F., et al. (2019) · PLoS ONE · doi:10.1371/journal.pone.0223543 · Cited by 61
Self-citation
Network-directed efficient isolation of previously uncultivated Chloroflexi and related bacteria in hot spring microbial mats
Xian, W.-D., Salam, N., Li, M., Zhou, E., Yin, Y.-R., Liu, Z., Ming, Y.-Z., Zhang, X., Wu, G., Liu, L., et al. (2020) · npj Biofilms and Microbiomes · doi:10.1038/s41522-020-0131-4 · Cited by 60
Gut Bacteria and Neuropsychiatric Disorders
Dicks, L. M. T., Hurn, D., & Hermanus, D. (2021) · Microorganisms · doi:10.3390/microorganisms9122583 · Cited by 63
Target Dysbiosis of Gut Microbes as a Future Therapeutic Manipulation in Alzheimer’s Disease
Zhu, F., Li, C., Chu, F., Tian, X., & Zhu, J. (2020) · Frontiers in Aging Neuroscience · doi:10.3389/fnagi.2020.544235 · Cited by 59
On detection thresholds–a review on diagnostic approaches in the infectious disease laboratory and the interpretation of their results
Hahn, A., Podbielski, A., Meyer, T., Zautner, A. E., Loderstädt, U., Schwarz, N. G., Krüger, A., Cadar, D., & Frickmann, H. (2020) · Acta Tropica · doi:10.1016/j.actatropica.2020.105377 · Cited by 51
Ribosome Biogenesis in Archaea
Londei, P., & Ferreira-Cerca, S. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.686977 · Cited by 49
Metagenomics and Other Omics Approaches to Bacterial Communities and Antimicrobial Resistance Assessment in Aquacultures
Nogueira, T., & Botelho, A. (2021) · Antibiotics · doi:10.3390/antibiotics10070787 · Cited by 51
Exploring the global vaginal microbiome and its impact on human health
Chacra, L. A., & Fenollar, F. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105172 · Cited by 47
A novel 3D in vitro model of the human gut microbiota
Biagini, F., Calvigioni, M., Lapomarda, A., Vecchione, A., Magliaro, C., Maria, C. D., Montemurro, F., Celandroni, F., Mazzantini, D., Mattioli‐Belmonte, M., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-78591-w · Cited by 44
A review of the resistome within the digestive tract of livestock
Ma, T., McAllister, T. A., & Guan, L. L. (2021) · Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology · doi:10.1186/s40104-021-00643-6 · Cited by 51
Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics
Li, C., Luan, Z., Zhao, Y., Chen, J., Yang, Y., Wang, C., Jing, Y., Qi, S., Li, Z., Guo, H., et al. (2022) · npj Biofilms and Microbiomes · doi:10.1038/s41522-022-00282-3 · Cited by 46
The modulatory effects of gut microbes and metabolites on blood-brain barrier integrity and brain function in sepsis-associated encephalopathy
Li, Z., Zhang, F., Sun, M., Liu, J., Zhao, L., Liu, S., Li, S., & Wang, B. (2023) · PeerJ · doi:10.7717/peerj.15122 · Cited by 43
“…classified into 11 different phyla, with Proteobacteria , Firmicutes , Actinobacteria , and Bacteroidetes comprising over 90% of the microbiome ( Bilen et al., 2018 ; Hugon et al., 2015 ; Li et al., 2014 ), while Fusobacteria and Verrucomicrobia phyla are present in low abundance ( Eckburg et…”
Isolation and Cultivation of Human Gut Microorganisms: A Review
Wan, X., Yang, Q., Wang, X., Bai, Y., & Liu, Z. (2023) · Microorganisms · doi:10.3390/microorganisms11041080 · Cited by 40
Dysbiosis and extraintestinal cancers
He, R., Qi, P., Shu, L.-Z., Ding, Y., Zeng, P., Wen, G., Xiong, Y., & Deng, H. (2025) · Journal of Experimental & Clinical Cancer Research · doi:10.1186/s13046-025-03313-x · Cited by 43
Exploring Gut Microbiota in Patients with Colorectal Disease Based on 16S rRNA Gene Amplicon and Shallow Metagenomic Sequencing
Liu, Y., Li, X., Yang, Y., Liu, Y., Wang, S., Ji, B., & Wei, Y. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2021.703638 · Cited by 36
The critical role of gut-brain axis microbiome in mental disorders
Basiji, K., Sendani, A. A., Ghavami, S. B., Farmani, M., Kazemifard, N., Sadeghi, A., Lotfali, E., & Aghdaei, H. A. (2023) · Metabolic Brain Disease · doi:10.1007/s11011-023-01248-w · Cited by 37
From Culturomics to Clinical Microbiology and Forward
Dubourg, G., Baron, S. A., Cadoret, F., Couderc, C., Fournier, P., Lagier, J., & Raoult, D. (2018) · Emerging infectious diseases · doi:10.3201/eid2409.170995 · Cited by 36
Self-citation
Updating the repertoire of cultured bacteria from the human being
Diakite, A., Dubourg, G., & Raoult, D. (2020) · Microbial Pathogenesis · doi:10.1016/j.micpath.2020.104698 · Cited by 35
Self-citation
Astrobiology of life on Earth
Hallsworth, J. E., Mancinelli, R. L., Conley, C. A., Dallas, T. D., Rinaldi, T., Dávila, A. F., Benison, K. C., Rapoport, A. I., Cavalazzi, B., Selbmann, L., et al. (2021) · Environmental Microbiology · doi:10.1111/1462-2920.15499 · Cited by 35
A droplet-based microfluidic approach to isolating functional bacteria from gut microbiota
Yin, J., Chen, X., Li, X., Kang, G., Wang, P., Song, Y., Ijaz, U. Z., Yin, H., & Huang, H. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.920986 · Cited by 35
Gut-muscle-brain axis: Molecular mechanisms in neurodegenerative disorders and potential therapeutic efficacy of probiotic supplementation coupled with exercise
Morella, I., Negro, M., Dossena, M., Brambilla, R., & D’Antona, G. (2023) · Neuropharmacology · doi:10.1016/j.neuropharm.2023.109718 · Cited by 36
The best of both worlds: a proposal for further integration of Candidatus names into the International Code of Nomenclature of Prokaryotes
Arahal, D. R., Bisgaard, M., Christensen, H. K., Clermont, D., Dijkshoorn, L., Duim, B., Emler, S., Figge, M. J., Göker, M., Moore, E. R. B., et al. (2024) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.006188 · Cited by 31
What the Gut Tells the Brain—Is There a Link between Microbiota and Huntington’s Disease?
Wronka, D., Karlik, A., Misiorek, J. O., & Przybył, Ł. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054477 · Cited by 32
Repertoire of Bacterial Species Cultured from the Human Oral Cavity and Respiratory Tract
Fonkou, M. D. M., Dufour, J.-C., Dubourg, G., & Raoult, D. (2018) · Future Microbiology · doi:10.2217/fmb-2018-0181 · Cited by 30
Self-citation
Functional gene-guided enrichment plus in situ microsphere cultivation enables isolation of new crucial ureolytic bacteria from the rumen of cattle
Liu, S., Yu, Z., Zhong, H., Zheng, N., Huws, S., Wang, J., & Zhao, S. (2023) · Microbiome · doi:10.1186/s40168-023-01510-4 · Cited by 29
Cardiovascular Disease May Be Triggered by Gut Microbiota, Microbial Metabolites, Gut Wall Reactions, and Inflammation
Dicks, L. M. T. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms251910634 · Cited by 26
Sequencing-guided re-estimation and promotion of cultivability for environmental bacteria
Zheng, M., Wen, L., He, C., Chen, X., Si, L., Li, H., Liang, Y., Zheng, W., & Guo, F. (2024) · Nature Communications · doi:10.1038/s41467-024-53446-4 · Cited by 30
“Bacterial Consortium”: A Potential Evolution of Fecal Microbiota Transplantation for the Treatment of Clostridioides difficile Infection
Quaranta, G., Ianiro, G., Maio, F. D., Guarnaccia, A., Fancello, G., Agrillo, C., Iannarelli, F., Bibbò, S., Amedei, A., Sanguinetti, M., et al. (2022) · BioMed Research International · doi:10.1155/2022/5787373 · Cited by 26
The Microbiota–Gut–Brain Axis: Key Mechanisms Driving Glymphopathy and Cerebral Small Vessel Disease
Nassir, C. M. N. C. M., Ramli, M. D. C., Ghazali, M. M., Jaffer, U., Hamid, H. A., Mehat, M. Z., & Hein, Z. M. (2024) · Life · doi:10.3390/life15010003 · Cited by 31
Impact of process temperature and organic loading rate on cellulolytic / hydrolytic biofilm microbiomes during biomethanation of ryegrass silage revealed by genome-centered metagenomics and metatranscriptomics
Maus, I., Klocke, M., Derenkó, J., Stolze, Y., Beckstette, M., Jost, C., Wibberg, D., Blom, J., Henke, C., Willenbücher, K., et al. (2020) · Environmental Microbiome · doi:10.1186/s40793-020-00354-x · Cited by 25
Taxonomic and Functional Dysregulation in Salivary Microbiomes During Oral Carcinogenesis
Chen, J.-W., Wu, J., Chiang, W.-F., Chen, Y., Wu, W.-S., & Wu, L. (2021) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2021.663068 · Cited by 26
Culturomics, a potential approach paving the way toward bacteriotherapy
Matar, G. M., & Bilen, M. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102194 · Cited by 24
Self-citation
Decoding the intestinal microbiota repertoire of sow and weaned pigs using culturomic and metagenomic approaches
Mun, D., Kim, H., Shin, M., Ryu, S., Song, M., Oh, S., & Kim, Y. (2021) · Journal of Animal Science and Technology · doi:10.5187/jast.2021.e124 · Cited by 23
An Integrated Multi-Disciplinary Perspective for Addressing Challenges of the Human Gut Microbiome
Shah, R., McKenzie, E. J., Rosin, M., Jadhav, S. R., Gondalia, S. V., Rosendale, D., & Beale, D. J. (2020) · Metabolites · doi:10.3390/metabo10030094 · Cited by 25
Untangling the web of intratumor microbiota in lung cancer
Liu, W. L., Xu, J., Pi, Z., Chen, Y., Jiang, G., Wan, Y., & Mao, W. (2023) · Biochimica et Biophysica Acta (BBA) - Reviews on Cancer · doi:10.1016/j.bbcan.2023.189025 · Cited by 27
Dietary Habits and Their Influence on the Microbiome and Mental Health in Adolescents
Sălcudean, A., Cîmpian, D. M., Popovici, R. A., Forna, N. C., Corodan-Comiati, D.-M., Sasu, A.-B., Cozma, M.-M., Bodo, C.-R., Enache, E.-C., Păcurar, M., et al. (2025) · Nutrients · doi:10.3390/nu17091496 · Cited by 27
Strategies and advancements in human microbiome description and the importance of culturomics
Bilen, M. (2020) · Microbial Pathogenesis · doi:10.1016/j.micpath.2020.104460 · Cited by 23
Self-citation
The urobiome, urinary tract infections, and the need for alternative therapeutics
Jones, J. A., Murphy, C. P., Sleator, R. D., & Culligan, E. P. (2021) · Microbial Pathogenesis · doi:10.1016/j.micpath.2021.105295 · Cited by 21
Over-feeding the gut microbiome: A scoping review on health implications and therapeutic perspectives
Barone, M., D’Amico, F., Fabbrini, M., Rampelli, S., Brigidi, P., & Turroni, S. (2021) · World Journal of Gastroenterology · doi:10.3748/wjg.v27.i41.7041 · Cited by 23
The functional microbiome of grapevine throughout plant evolutionary history and lifetime
Fournier, P., Pellan, L., Barroso‐Bergadà, D., Bohan, D. A., Candresse, T., Delmotte, F., Dufour, M., Lauvergeat, V., Marrec, C. L., Marais, A., et al. (2022) · Advances in ecological research/Advances in Ecological Research · doi:10.1016/bs.aecr.2022.09.001 · Cited by 27
Culturing the Human Oral Microbiota, Updating Methodologies and Cultivation Techniques
Khelaifia, S., Pilliol, V., Belkacemi, S., Tassery, H., Terrer, E., & Aboudharam, G. (2023) · Microorganisms · doi:10.3390/microorganisms11040836 · Cited by 23
Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages
Fusco, V., Fanelli, F., & Chieffi, D. (2023) · Foods · doi:10.3390/foods12203782 · Cited by 23
Application of LpxC enzyme inhibitor to inhibit some fast-growing bacteria in human gut bacterial culturomics
Hou, F., Chang, Y., Huang, Z., Han, N., Bin, L., Deng, H., Li, Z., Pan, Z., Ding, L., Gao, H., et al. (2019) · BMC Microbiology · doi:10.1186/s12866-019-1681-6 · Cited by 21
Tackling Intrinsic Antibiotic Resistance in Serratia marcescens with a Combination of Ampicillin/Sulbactam and Phage SALSA
Weber, L., Jansen, M., Krüttgen, A., Buhl, E. M., & Horz, H. (2020) · Antibiotics · doi:10.3390/antibiotics9070371 · Cited by 21
Human milk microbiota: what did we learn in the last 20 years?
Selma‐Royo, M., Calvo‐Lerma, J., Bäuerl, C., Esteban-Torres, M., Cabrera‐Rubio, R., & Collado, M. C. (2022) · Microbiome Research Reports · doi:10.20517/mrr.2022.05 · Cited by 23
Isolation and preliminary screening of potentially probiotic Weissella confusa strains from healthy human feces by culturomics
Wang, W., Liu, W., & Chu, W. (2020) · Microbial Pathogenesis · doi:10.1016/j.micpath.2020.104356 · Cited by 21
Prevotella hominis sp. nov., isolated from human faeces
Liou, J.-S., Huang, C., Ikeyama, N., Lee, A.-Y., Chen, I.-C., Blom, J., Chen, C.-C., Chen, C.-H., Lin, Y., Hsieh, S., et al. (2020) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.004342 · Cited by 23
The impact of novel probiotics isolated from the human gut on the gut microbiota and health
Caesar, R. (2024) · Diabetes Obesity and Metabolism · doi:10.1111/dom.16129 · Cited by 22
Cultivation of Diverse Microorganisms from Hypersaline Lake and Impact of Delay in Sample Processing on Cell Viability
Kajale, S. C., Deshpande, N. M., Shouche, Y. S., & Sharma, A. (2020) · Current Microbiology · doi:10.1007/s00284-019-01857-8 · Cited by 20
Gut Microbiome Interventions: From Dysbiosis to Next-Generation Probiotics (NGPs) for Disease Management
Gupta, M. K., & Srivastava, R. (2025) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-025-10582-7 · Cited by 23
Culturomics Approach to Identify Diabetic Foot Infection Bacteria
Złoch, M., Sibińska, E., Kupczyk, W., Jackowski, M., Pomastowski, P., & Buszewski, B. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22179574 · Cited by 19
Next-Generation Probiotics - The Future of Biotherapeutics
(2022) · Microbial Bioactives · doi:10.25163/microbbioacts.514309 · Cited by 21
Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study
Yadav, A., Ahlawat, S., & Sharma, K. K. (2023) · Journal of Applied Microbiology · doi:10.1093/jambio/lxad280 · Cited by 18
Metabolic Phenotypes as Potential Biomarkers for Linking Gut Microbiome With Inflammatory Bowel Diseases
Iablokov, S. N., Klimenko, N. S., Efimova, D. A., Shashkova, T., Novichkov, P. S., Rodionov, D. A., & Tyakht, A. (2021) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.603740 · Cited by 19
Traditional Probiotics, Next-Generation Probiotics and Engineered Live Biotherapeutic Products in Chronic Wound Healing
Kaistha, S. D., & Deshpande, N. M. (2021) · Springer eBooks · doi:10.1007/978-981-16-2677-7_8 · Cited by 19
Koch Postulate: Why Should we Grow Bacteria?
Lagier, J., Dubourg, G., Amrane, S., & Raoult, D. (2017) · Archives of Medical Research · doi:10.1016/j.arcmed.2018.02.003 · Cited by 17
Self-citation
EXPRESSION OF CONCERN: Noncontiguous finished genome sequence and description of Raoultibacter massiliensis gen. nov., sp. nov. and Raoultibacter timonensis sp. nov, two new bacterial species isolated from the human gut
Traore, S. I., Bilen, M., Beye, M., Diop, A., Fonkou, M. D. M., Tall, M. L., Michelle, C., Yasir, M., Azhar, E. I., Bibi, F., et al. (2019) · MicrobiologyOpen · doi:10.1002/mbo3.758 · Cited by 17
Self-citation
The endocannabinoid system: a bridge between alzheimer’s disease and gut microbiota
Bisogno, T., Lauritano, A., & Piscitelli, F. (2021) · Life · doi:10.3390/life11090934 · Cited by 16
Coupling culturomics and metagenomics sequencing to characterize the gut microbiome of patients with cancer treated with immune checkpoint inhibitors
Diop, K., Mbaye, B., Nili, S., Filin, A., Benlaïfaoui, M., Malo, J., Renaud, A. S., Belkaïd, W., Hunter, S., Messaoudene, M., et al. (2025) · Gut Pathogens · doi:10.1186/s13099-025-00694-4 · Cited by 15
Culturomics: A critical approach in studying the roles of human and animal microbiota
Howe, S. M., Liu, Z., Zuo, B., & Zhao, J. (2024) · Animal Nutriomics · doi:10.1017/anr.2024.6 · Cited by 16
Virus and microbiota relationships in humans and other mammals: An evolutionary view
Lima, M. T., Andrade, A. C. D. S. P., Oliveira, G. P., Nicoli, J. R., Martins, F. S., Kroon, E. G., & Abrahão, J. S. (2019) · Human Microbiome Journal · doi:10.1016/j.humic.2018.11.001 · Cited by 16
Multi-Omics Approaches: The Key to Improving Respiratory Health in People With Cystic Fibrosis?
Lee, A. J., Einarsson, G. G., Gilpin, D. F., & Tunney, M. M. (2020) · Frontiers in Pharmacology · doi:10.3389/fphar.2020.569821 · Cited by 14
Culturing and Molecular Approaches for Identifying Microbiota Taxa Impacting Children’s Obesogenic Phenotypes Related to Xenobiotic Dietary Exposure
López‐Moreno, A., Ruiz-Moreno, Á., Pardo-Cacho, J., Cerk, K., Torres-Sánchez, A., Ortíz, P., Úbeda, M., & Aguilera, J. (2022) · Nutrients · doi:10.3390/nu14020241 · Cited by 15

Authors: Bilen, M., Dufour, J.-C., Lagier, J.-C., Cadoret, F., Daoud, Z., Dubourg, G., & Raoult, D.
Affiliations: University of Balamand (LB)
Inserm (FR)
Aix-Marseille Université (FR)
Assistance Publique Hôpitaux de Marseille (FR)
King Abdulaziz University (SA)
Corresponding author: Raoult, Didier
ORCID: Bilen, Melhem
Dufour, Jean-Charles
Lagier, Jean-Christophe
Cadoret, Fréderic
Daoud, Ziad
Raoult, Didier
Venue: Microbiome
Publisher: Springer Science and Business Media LLC
Published: 2018-05-24
Volume: 6
Issue: 1
Pages: 94-94
ISSN: 2049-2618 (ISSN-L)
DOI: 10.1186/s40168-018-0485-5
PMC: PMC5966928
OpenAlex: W2807527107
Cited by: 231
References: 90
Citations by year: 2026: 15 · 2025: 19 · 2024: 28 · 2023: 38 · 2022: 27 · 2021: 26 · 2020: 36 · 2019: 31 · 2018: 10
FWCI: 2.53
Type: journal article
Language: en
Open access: gold
doi.org
Licence: cc-by
creativecommons.org/licenses/by/4.0/ (tdm)
Locations: Microbiome (publishedVersion, cc-by)
Europe PMC (PubMed Central) (publishedVersion, other-oa)
PubMed Central (publishedVersion, cc-by)
PubMed (publishedVersion)
HAL (submittedVersion, other-oa)
DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders: IHU Méditerranée Infection
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gut microbiota and health
Physical Sciences › Environmental Science › Ecology › Microbial Community Ecology and Physiology
Health Sciences › Medicine › Microbiology (medical) › Bacterial Identification and Susceptibility Testing
Keywords: culturomics, human microbiota, new species, Firmicutes, Proteobacteria, Bacteroidetes, actinobacteria
MeSH terms: Firmicutes, Bacillota, Gastrointestinal Microbiome, Archaea, Bacteria, DNA, Bacterial, Humans, DNA, Archaeal, Proteobacteria, Actinobacteria, Bacteroidetes, Metagenomics

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

The contribution of culturomics to the repertoire of isolated human bacterial and archaeal species

Abstract

Overview

Integrity signals

Figures

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks