The food-gut axis: lactic acid bacteria and their link to food, the gut microbiome and human health

DADA2: High–resolution sample inference from Illumina amplicon data

Callahan, B. J., McMurdie, P. J., Rosen, M. J., Han, A. W., Johnson, A. J. A., & Holmes, S. P. (2016) · Nature Methods · doi:10.1038/nmeth.3869 · Cited by 35,698 · see citing works

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

Bolyen, E., Rideout, J. R., Dillon, M. R., Bokulich, N. A., Abnet, C. C., Al-Ghalith, G. A., Alexander, H., Alm, E. J., Arumugam, M., Asnicar, F., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0209-9 · Cited by 23,742 · see citing works

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

Schloss, P. D., Westcott, S. L., Ryabin, T., Hall, J. R., Hartmann, M., Hollister, E. B., Lesniewski, R. A., Oakley, B. B., Parks, D. H., Robinson, C. J., et al. (2009) · Applied and Environmental Microbiology · doi:10.1128/aem.01541-09 · Cited by 20,966 · see citing works

Prokka: rapid prokaryotic genome annotation

Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,512 · see citing works

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

Simão, F. A., Waterhouse, R. M., Ioannidis, P., Kriventseva, E. V., & Zdobnov, E. M. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv351 · Cited by 13,344 · see citing works

CheckM: Assessing the Quality of Microbial Genomes Recovered from Isolates, Single Cells, and Metagenomes

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015) · Genome Research · doi:10.1101/gr.186072.114 · Cited by 12,496 · see citing works

Structure, function and diversity of the healthy human microbiome

The Human Microbiome Project Consortium (2012) · Nature · doi:10.1038/nature11234 · Cited by 11,726 · see citing works

A human gut microbial gene catalogue established by metagenomic sequencing

MetaHIT Consortium, Qin, J., Li, R., Raes, J., Arumugam, M., Burgdorf, K. S., Manichanh, C., Nielsen, T., Pons, N., Levenez, F., et al. (2010) · Nature · doi:10.1038/nature08821 · Cited by 11,624 · see citing works

Diet rapidly and reproducibly alters the human gut microbiome

David, L. A., Maurice, C. F., Carmody, R. N., Gootenberg, D. B., Button, J. E., Wolfe, B. E., Ling, A. V., Devlin, A. S., Varma, Y., Fischbach, M. A., et al. (2014) · Nature · doi:10.1038/nature12820 · Cited by 10,100 · see citing works

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv033 · Cited by 9,781 · see citing works

Untitled work

Hill (2014) · doi:10.1038/nrgastro.2014.66 · Cited by 9,592 · see citing works

Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences

Langille, M. G. I., Zaneveld, J., Caporaso, J. G., McDonald, D., Knights, D., Reyes, J. A., Clemente, J. C., Burkepile, D. E., Vega Thurber, R. L., Knight, R., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2676 · Cited by 9,116 · see citing works

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 · see citing works

Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

Yoon, S.-H., Ha, S. M., Kwon, S., Lim, J., Kim, Y.-S., Seo, H., & Chun, J. (2016) · INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY · doi:10.1099/ijsem.0.001755 · Cited by 7,733 · see citing works

Changes of Intestinal Functions in Liver Cirrhosis

Fukui, H., & Wiest, R. (2016) · Inflammatory Intestinal Diseases · doi:10.1159/000444436 · Cited by 6,820 · see citing works

SILVA: a comprehensive online resource for quality checked and aligned ribosomal RNA sequence data compatible with ARB

Pruesse, E., Quast, C., Knittel, K., Fuchs, B. M., Ludwig, W., Peplies, J., & Glöckner, F. O. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm864 · Cited by 6,682 · see citing works

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 · see citing works

Role of the microbiota in immunity and inflammation.

Belkaid, Y., & Hand, T. W. (2014) · Cell · doi:10.1016/j.cell.2014.03.011 · Cited by 5,385 · see citing works

Host-Bacterial Mutualism in the Human Intestine

Bäckhed, F., Ley, R. E., Sonnenburg, J. L., Peterson, D. A., & Gordon, J. I. (2005) · Science · doi:10.1126/science.1104816 · Cited by 5,277 · see citing works

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

McDonald, D. T., Price, M. N., Goodrich, J. K., Nawrocki, E. P., DeSantis, T. Z., Probst, A. J., Andersen, G. L., Knight, R. D., & Hugenholtz, P. (2011) · The ISME Journal · doi:10.1038/ismej.2011.139 · Cited by 5,010 · see citing works

Richness of human gut microbiome correlates with metabolic markers

Le Chatelier, E., Nielsen, T., Qin, J., Prifti, E., Hildebrand, F., Falony, G., Almeida, M., Arumugam, M., Batto, J.-M., Kennedy, S., et al. (2013) · Nature · doi:10.1038/nature12506 · Cited by 4,662 · see citing works

Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases

Frank, D. N., St. Amand, A. L., Feldman, R. A., Boedeker, E. C., Harpaz, N., & Pace, N. R. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0706625104 · Cited by 4,611 · see citing works

Kraken: ultrafast metagenomic sequence classification using exact alignments

Wood, D. E., & Salzberg, S. L. (2014) · Genome Biology · doi:10.1186/gb-2014-15-3-r46 · Cited by 4,521 · see citing works

metaSPAdes: a new versatile metagenomic assembler

Nurk, S., Meleshko, D., Korobeynikov, A., & Pevzner, P. A. (2017) · Genome Research · doi:10.1101/gr.213959.116 · Cited by 4,496 · see citing works

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352 · see citing works

Ribosomal Database Project: data and tools for high throughput rRNA analysis

Cole, J. R., Wang, Q., Fish, J. A., Chai, B., McGarrell, D. M., Sun, Y., Brown, C. T., Porras‐Alfaro, A., Kuske, C. R., & Tiedje, J. M. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt1244 · Cited by 4,322 · see citing works

MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies

Kang, D., Li, F., Kirton, E., Thomas, A., Egan, R. S., An, H., & Wang, Z. (2019) · PeerJ · doi:10.7717/peerj.7359 · Cited by 3,784 · see citing works

A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life

Parks, D. H., Chuvochina, M., Waite, D. W., Rinke, C., Skarshewski, A., Chaumeil, P.-A., & Hugenholtz, P. (2018) · Nature Biotechnology · doi:10.1038/nbt.4229 · Cited by 3,603 · see citing works

Orchestrating high-throughput genomic analysis with Bioconductor

Huber, W. K., Carey, V. J., Gentleman, R. C., Anders, S., Carlson, M. R. J., Carvalho, B. S., Bravo, H. C., Davis, S. R., Gatto, L., Girke, T., et al. (2015) · Nature Methods · doi:10.1038/nmeth.3252 · Cited by 3,499 · see citing works

A taxonomic note on the genus lactobacillus: description of 23 novel genera, emended description of the genus lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae

Zheng, J., Wittouck, S., Salvetti, E., Franz, C. M. A. P., Harris, H. M. B., Mattarelli, P., O’Toole, P. W., Pot, B., Vandamme, P., Walter, J., et al. (2020) · International Journal of Systematic and Evolutionary Microbiology · doi:10.1099/ijsem.0.004107 · Cited by 3,313 · see citing works

Gut metagenome in European women with normal, impaired and diabetic glucose control

Karlsson, F. H., Tremaroli, V., Nookaew, I., Bergström, G., Behre, C. J., Fagerberg, B., Nielsen, J., & Bäckhed, F. (2013) · Nature · doi:10.1038/nature12198 · Cited by 3,115 · see citing works

Gut Microbiota in Human Adults with Type 2 Diabetes Differs from Non-Diabetic Adults

Larsen, N., Vogensen, F. K., van den Berg, F. W. J., Nielsen, D. S., Andreasen, A. S., Pedersen, B. K., Al-Soud, W. A., Sørensen, S. J., Hansen, L. H., & Jakobsen, M. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009085 · Cited by 2,952 · see citing works

Structure and function of the global ocean microbiome

Sunagawa, S., Coelho, L. P., Chaffron, S., Kultima, J. R., Labadie, K., Salazar, G., Djahanschiri, B., Zeller, G., Mende, D. R., Alberti, A., et al. (2015) · Science · doi:10.1126/science.1261359 · Cited by 2,945 · see citing works

The gut flora as a forgotten organ

O'Hara, A. M., & Shanahan, F. (2006) · The EMBO Reports · doi:10.1038/sj.embor.7400731 · Cited by 2,791 · see citing works

Binning metagenomic contigs by coverage and composition

Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014) · Nature Methods · doi:10.1038/nmeth.3103 · Cited by 2,707 · see citing works

A communal catalogue reveals Earth's multiscale microbial diversity

Thompson, L. R., Sanders, J. G., McDonald, D., Amir, A., Ladau, J., Locey, K. J., Prill, R. J., Tripathi, A., Gibbons, S. M., Ackermann, G., et al. (2017) · Nature · doi:10.1038/nature24621 · Cited by 2,684 · see citing works

Changes in diet and lifestyle and long-term weight gain in women and men

Mozaffarian, D., Hao, T., Rimm, E. B., Willett, W. C., & Hu, F. B. (2011) · New England Journal of Medicine · doi:10.1056/nejmoa1014296 · Cited by 2,527 · see citing works

Origins and evolution of the Western diet: health implications for the 21st century1,2

Cordain, L., Eaton, S. B., Sebastian, A., Mann, N., Lindeberg, S., Watkins, B. A., O’Keefe, J. H., & Brand-Miller, J. (2005) · The American Journal of Clinical Nutrition · doi:10.1093/ajcn.81.2.341 · Cited by 2,397 · see citing works

Shotgun metagenomics, from sampling to analysis

Quince, C., Walker, A. W., Simpson, J. T., Loman, N. J., & Segata, N. (2017) · Nature Biotechnology · doi:10.1038/nbt.3935 · Cited by 2,202 · see citing works

MetaPhlAn2 for enhanced metagenomic taxonomic profiling

Truong, D. T., Franzosa, E. A., Tickle, T. L., Scholz, M., Weingart, G., Pasolli, E., Tett, A., Huttenhower, C., & Segata, N. (2015) · Nature Methods · doi:10.1038/nmeth.3589 · Cited by 2,185 · see citing works

Disentangling type 2 diabetes and metformin treatment signatures in the human gut microbiota

MetaHIT consortium, Forslund, K., Hildebrand, F., Nielsen, T., Falony, G., Le Chatelier, E., Sunagawa, S., Prifti, E., Vieira-Silva, S., Gudmundsdottir, V., et al. (2015) · Nature · doi:10.1038/nature15766 · Cited by 2,116 · see citing works

Probiotics and prebiotics in intestinal health and disease: from biology to the clinic

Sanders, M. E., Merenstein, D. J., Reid, G., Gibson, G. R., & Rastall, R. A. (2019) · Nature Reviews Gastroenterology & Hepatology · doi:10.1038/s41575-019-0173-3 · Cited by 2,059 · see citing works

Recovery of nearly 8,000 metagenome-assembled genomes substantially expands the tree of life

Parks, D. H., Rinke, C., Chuvochina, M., Chaumeil, P.-A., Woodcroft, B. J., Evans, P. N., Hugenholtz, P., & Tyson, G. W. (2017) · Nature Microbiology · doi:10.1038/s41564-017-0012-7 · Cited by 1,882 · see citing works

Guidelines for the evaluation of probiotics in food

Who, F. (2002) · Medical Entomology and Zoology · Cited by 1,843 · see citing works

Dietary intervention impact on gut microbial gene richness

Cotillard, A., Kennedy, S. P., Kong, L. C., Prifti, E., Pons, N., Le Chatelier, E., Almeida, M., Quinquis, B., Levenez, F., Galleron, N., et al. (2013) · Nature · doi:10.1038/nature12480 · Cited by 1,832 · see citing works

Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

(2017) · doi:10.1038/s41564-018-0171-1 · Cited by 1,742 · see citing works

Personalized Gut Mucosal Colonization Resistance to Empiric Probiotics Is Associated with Unique Host and Microbiome Features

Zmora, N., Zilberman-Schapira, G., Suez, J., Mor, U., Dori-Bachash, M., Bashiardes, S., Kotler, E., Zur, M., Regev-Lehavi, D., Brik, R. B.-Z., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.041 · Cited by 1,695 · cited 2× · see citing works

Species-level functional profiling of metagenomes and metatranscriptomes

Franzosa, E. A., McIver, L. J., Rahnavard, G., Thompson, L. R., Schirmer, M., Weingart, G., Lipson, K. S., Knight, R., Caporaso, J. G., Segata, N., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0176-y · Cited by 1,693 · see citing works

The oral and gut microbiomes are perturbed in rheumatoid arthritis and partly normalized after treatment

Zhang, X., Zhang, D., Jia, H., Feng, Q., Wang, D., Liang, D., Wu, X., Li, J., Tang, L., Li, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3914 · Cited by 1,690 · see citing works

Health benefits of fermented foods: Microbiota and beyond

Marco, M. L., Heeney, D., Binda, S., Cifelli, C. J., Cotter, P. D., Foligné, B., Gänzle, M., Kort, R., Pasin, G., Pihlanto, A., et al. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2016.11.010 · Cited by 1,674 · see citing works

Extensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle

Pasolli, E., Asnicar, F., Manara, S., Zolfo, M., Karcher, N., Armanini, F., Beghini, F., Manghi, P., Tett, A., Ghensi, P., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.001 · Cited by 1,591 · see citing works

A complete domain-to-species taxonomy for Bacteria and Archaea

Parks, D. H., Chuvochina, M. S., Chaumeil, P.-A., Rinke, C., Mussig, A. J., & Hugenholtz, P. (2020) · Nature Biotechnology · doi:10.1038/s41587-020-0501-8 · Cited by 1,542 · see citing works

Direct analysis of genes encoding 16S rRNA from complex communities reveals many novel molecular species within the human gut

Suau, A., Bonnet, R., Sutren, M., Godon, J.-J., Gibson, G. R., Collins, M. D., & Doré, J. (1999) · Applied and Environmental Microbiology · doi:10.1128/aem.65.11.4799-4807.1999 · Cited by 1,490 · see citing works

Human gut microbiome: Hopes, threats and promises

Cani, P. D. (2018) · Gut · doi:10.1136/gutjnl-2018-316723 · Cited by 1,386 · see citing works

A new genomic blueprint of the human gut microbiota

Almeida, A., Mitchell, A. L., Boland, M., Forster, S. C., Gloor, G. B., Tarkowska, A., Lawley, T. D., & Finn, R. D. (2019) · Nature · doi:10.1038/s41586-019-0965-1 · Cited by 1,314 · see citing works

Scopus database: a review

Burnham, J. F. (2006) · Biomedical Digital Libraries · doi:10.1186/1742-5581-3-1 · Cited by 1,287 · see citing works

Consumption of fermented milk product with probiotic modulates brain activity

Tillisch, K., Labus, J., Kilpatrick, L., Jiang, Z., Stains, J., Ebrat, B., Guyonnet, D., Legrain–Raspaud, S., Trotin, B., Naliboff, B., et al. (2013) · Gastroenterology · doi:10.1053/j.gastro.2013.02.043 · Cited by 1,192 · see citing works

Bile Salt Hydrolase Activity in Probiotics

Begley, M., Hill, C., & Gahan, C. G. M. (2006) · Applied and Environmental Microbiology · doi:10.1128/aem.72.3.1729-1738.2006 · Cited by 1,187 · see citing works

Post-Antibiotic Gut Mucosal Microbiome Reconstitution Is Impaired by Probiotics and Improved by Autologous FMT

Suez, J., Zmora, N., Zilberman-Schapira, G., Mor, U., Dori-Bachash, M., Bashiardes, S., Zur, M., Regev-Lehavi, D., Ben-Zeev Brik, R., Federici, S., et al. (2018) · Cell · doi:10.1016/j.cell.2018.08.047 · Cited by 1,184 · see citing works

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403

Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.gr-1697r · Cited by 1,139 · see citing works

The Complete Genome Sequence of the Lactic Acid Bacterium Lactococcus lactis ssp. lactis IL1403Preprint

Bolotin, A., Wincker, P., Mauger, S., Jaillon, O., Malarme, K., Weissenbach, J., Ehrlich, S. D., & Sorokin, A. (2001) · Genome Research · doi:10.1101/gr.169701 · Cited by 1,133 · see citing works

Postbiotics: An Evolving Term within the Functional Foods Field

Aguilar-Toalá, J. E., Garcia-Varela, R., Garcia, H. S., Mata-Haro, V., González-Córdova, A. F., Vallejo-Cordoba, B., & Hernández-Mendoza, A. (2018) · Trends in Food Science & Technology · doi:10.1016/j.tifs.2018.03.009 · Cited by 1,078 · see citing works

Development of an extensive set of 16S rDNA-targeted primers for quantification of pathogenic and indigenous bacteria in faecal samples by real-time PCR

Rinttilä, T., Kassinen, A., Malinen, E., Krogius-Kurikka, L., & Palva, A. (2004) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2004.02409.x · Cited by 1,018 · see citing works

Microbial community profiling for human microbiome projects: Tools, techniques, and challengesPreprint

Hamady, M., & Knight, R. D. (2009) · Genome Research · doi:10.1101/gr.085464.108 · Cited by 998 · see citing works

Meta-analysis of gut microbiome studies identifies disease-specific and shared responses

(2017) · doi:10.1038/s41467-017-01973-8 · Cited by 986 · see citing works

Multiple sclerosis patients have a distinct gut microbiota compared to healthy controls

Chen, J., Chia, N., Kalari, K. R., Yao, J. Z., Novotna, M., Paz Soldan, M. M., Luckey, D. H., Marietta, E. V., Jeraldo, P. R., Chen, X., et al. (2016) · Scientific Reports · doi:10.1038/srep28484 · Cited by 933 · see citing works

The sequence read archive: explosive growth of sequencing data

Kodama, Y., Shumway, M., Leinonen, R., & on behalf of the International Nucleotide Sequence Database Collaboration (2012) · Nucleic Acids Research · doi:10.1093/nar/gkr854 · Cited by 894 · see citing works

Bacteriocin production as a mechanism for the antiinfective activity of <i>Lactobacillus salivarius</i> UCC118

Corr, S. C., Li, Y., Riedel, C. U., O'Toole, P. W., Hill, C., & Gahan, C. G. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0700440104 · Cited by 853 · see citing works

Microbial strain-level population structure and genetic diversity from metagenomes

Truong, D. T., Tett, A., Pasolli, E., Huttenhower, C., & Segata, N. (2017) · Genome Research · doi:10.1101/gr.216242.116 · Cited by 839 · see citing works

Defining a Healthy Human Gut Microbiome: Current Concepts, Future Directions, and Clinical Applications

Bäckhed, F., Fraser, C. M., Ringel, Y., Sanders, M. E., Sartor, R. B., Sherman, P. M., Versalovic, J., Young, V., & Finlay, B. B. (2012) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2012.10.012 · Cited by 836 · see citing works

Inflammation, antibiotics, and diet as environmental stressors of the gut microbiome in pediatric Crohn's disease

Lewis, J. D., Chen, E. Z., Baldassano, R. N., Otley, A. R., Griffiths, A. M., Lee, D., Bittinger, K., Bailey, A., Friedman, E. S., Hoffmann, C., et al. (2015) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823 · see citing works

Safety assessment of probiotics for human use

Sanders, M. E., Akkermans, L. M. A., Haller, D., Hammerman, C., Heimbach, J. T., Hörmannsperger, G., & Huys, G. (2010) · Gut Microbes · doi:10.4161/gmic.1.3.12127 · Cited by 816 · see citing works

Fermented foods: definitions and characteristics, impact on the gut microbiota and effects on gastrointestinal health and disease

Dimidi, E., Cox, S., Rossi, M., & Whelan, K. (2019) · Nutrients · doi:10.3390/nu11081806 · Cited by 801 · cited 1× · see citing works

US immigration westernizes the human gut microbiome

Vangay, P., Johnson, A. J., Ward, T. L., Al-Ghalith, G. A., Shields-Cutler, R. R., Hillmann, B. M., Lucas, S. K., Beura, L. K., Thompson, E. A., Till, L. M., et al. (2018) · Cell · doi:10.1016/j.cell.2018.10.029 · Cited by 794 · see citing works

Health benefits of fermented foods

Şanlier, N., Gökcen, B. B., & Sezgin, A. C. (2019) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2017.1383355 · Cited by 789 · see citing works

Detection of Lactobacillus, Pediococcus, Leuconostoc , and Weissella Species in Human Feces by Using Group-Specific PCR Primers and Denaturing Gradient Gel Electrophoresis

Walter, J., Hertel, C., Tannock, G. W., Lis, C. M., Munro, K., & Hammes, W. P. (2001) · Applied and Environmental Microbiology · doi:10.1128/aem.67.6.2578-2585.2001 · Cited by 782 · see citing works

Understanding the effects of diet on bacterial metabolism in the large intestine

Louis, P., Scott, K. P., Duncan, S. H., & Flint, H. J. (2007) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2007.03322.x · Cited by 775 · see citing works

Ecological Role of Lactobacilli in the Gastrointestinal Tract: Implications for Fundamental and Biomedical Research

Walter, J. (2008) · Applied and Environmental Microbiology · doi:10.1128/aem.00753-08 · Cited by 756 · see citing works

New insights from uncultivated genomes of the global human gut microbiome

Nayfach, S., Shi, Z. J., Seshadri, R., Pollard, K. S., & Kyrpides, N. C. (2019) · Nature · doi:10.1038/s41586-019-1058-x · Cited by 737 · see citing works

Fermented foods in a global age: east meets West

Tamang, J. P., Cotter, P. D., Endo, A., Han, N. S., Kort, R., Liu, S. Q., Mayo, B., Westerik, N., & Hutkins, R. (2020) · Comprehensive Reviews in Food Science and Food Safety · doi:10.1111/1541-4337.12520 · Cited by 719 · see citing works

Probiotics and prebiotic galacto-oligosaccharides in the prevention of allergic diseases: A randomized, double-blind, placebo-controlled trial

Kukkonen, A. K., Savilahti, E., Haahtela, T., Juntunen‐Backman, K., Korpela, R., Poussa, T. A., Tuure, T., & Kuitunen, M. (2006) · Journal of Allergy and Clinical Immunology · doi:10.1016/j.jaci.2006.09.009 · Cited by 708 · see citing works

Bacteriocin Production: a Probiotic Trait?

Dobson, A., Cotter, P. D., Ross, R. P., & Hill, C. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.05576-11 · Cited by 690 · see citing works

Probiotic yogurt improves antioxidant status in type 2 diabetic patients

Ejtahed, H. S., Mohtadi-Nia, J., Homayouni-Rad, A., Niafar, M., Asghari-Jafarabadi, M., & Mofid, V. (2012) · Nutrition · doi:10.1016/j.nut.2011.08.013 · Cited by 683 · see citing works

A randomized controlled trial to test the effect of multispecies probiotics on cognitive reactivity to sad mood

Steenbergen, L., Sellaro, R., van Hemert, S., Bosch, J. A., & Colzato, L. S. (2015) · Brain, Behavior, and Immunity · doi:10.1016/j.bbi.2015.04.003 · Cited by 671 · see citing works

Analysis of the Fecal Microflora of Human Subjects Consuming a Probiotic Product Containing Lactobacillus rhamnosus DR20

Tannock, G. W., Munro, K., Harmsen, H. J. M., Welling, G. W., Smart, J., & Gopal, P. K. (2000) · Applied and Environmental Microbiology · doi:10.1128/aem.66.6.2578-2588.2000 · Cited by 671 · see citing works

Traditional Cheeses: Rich and Diverse Microbiota with Associated Benefits

Montel, M.-C., Buchin, S., Mallet, A., Delbes-Paus, C., Vuitton, D. A., Desmasures, N., & Berthier, F. (2014) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2014.02.019 · Cited by 665 · see citing works

Oligotyping: differentiating between closely related microbial taxa using 16S rRNA gene data

Eren, A. M., Maignien, L., Sul, W. J., Murphy, L. G., Grim, S. L., Morrison, H. G., & Sogin, M. L. (2013) · Methods in Ecology and Evolution · doi:10.1111/2041-210x.12114 · Cited by 620 · see citing works

Fate, activity, and impact of ingested bacteria within the human gut microbiota

Derrien, M., & van Hylckama Vlieg, J. E. T. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.03.002 · Cited by 605 · see citing works

Qiita: rapid, web-enabled microbiome meta-analysis

Gonzalez, A., Navas-Molina, J. A., Kościółek, T., McDonald, D. T., Vázquez‐Baeza, Y., Ackermann, G. L., DeReus, J., Janssen, S., Swafford, A. D.-E., Orchanian, S. B., et al. (2018) · Nature Methods · doi:10.1038/s41592-018-0141-9 · Cited by 594 · see citing works

Compendium of 4,941 rumen metagenome-assembled genomes for rumen microbiome biology and enzyme discovery

Stewart, R. D., Auffret, M. D., Warr, A., Walker, A. W., Roehe, R., & Watson, M. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0202-3 · Cited by 593 · see citing works

Lactic acid bacteria contribution to gut microbiota complexity: lights and shadows.

Pessione, E. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00086 · Cited by 592 · see citing works

Functions and emerging applications of bacteriocins

Chikindas, M. L., Weeks, R. M., Drider, D., Chistyakov, V. A., & Dicks, L. M. T. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.07.011 · Cited by 574 · see citing works

S layer protein A of Lactobacillus acidophilus NCFM regulates immature dendritic cell and T cell functions

Konstantinov, S. R., Smidt, H., de Vos, W. M., Bruijns, S. C. M., Singh, S., Valence, F., Mollé, D., Lortal, S., Altermann, E., Klaenhammer, T. R., et al. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810305105 · Cited by 568 · see citing works

MGnify: the microbiome analysis resource in 2020

Mitchell, A. L., Almeida, A., Beracochea, M., Boland, M., Burgin, J., Cochrane, G., Crusoe, M. R., Kale, V., Potter, S. C., Richardson, L. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1035 · Cited by 562 · see citing works

Assembly of 913 microbial genomes from metagenomic sequencing of the cow rumen

Stewart, R. D., Auffret, M. D., Warr, A., Wiser, A. H., Press, M. O., Langford, K. W., Liachko, I., Snelling, T. J., Dewhurst, R. J., Walker, A. W., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-03317-6 · Cited by 559 · see citing works

Lifestyles in transition: evolution and natural history of the genus Lactobacillus

Duar, R. M., Lin, X. B., Zheng, J., Martino, M. E., Grenier, T., Pérez-Muñoz, M. E., Leulier, F., Gänzle, M. G., & Walter, J. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux030 · Cited by 554 · see citing works

How to select a probiotic? A review and update of methods and criteria

Pereira, G. V. D. M., Coelho, B. D. O., Magalhães, A. I., Thomaz‐Soccol, V., & Soccol, C. R. (2018) · Biotechnology Advances · doi:10.1016/j.biotechadv.2018.09.003 · Cited by 545 · see citing works

Expanding the biotechnology potential of lactobacilli through comparative genomics of 213 strains and associated genera

Sun, Z., Harris, H. M. B., McCann, A., Guo, C., Argimón, S., Zhang, W., Yang, X., Jeffery, I. B., Cooney, J. C., Kagawa, T. F., et al. (2015) · Nature Communications · doi:10.1038/ncomms9322 · Cited by 543 · see citing works

Fermented Foods as a Dietary Source of Live Organisms

Rezac, S., Kok, C. R., Heermann, M., & Hutkins, R. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.01785 · Cited by 540 · see citing works

Effect of probiotic and prebiotic vs placebo on psychological outcomes in patients with major depressive disorder: a randomized clinical trial

Kazemi, A., Noorbala, A. A., Azam, K., Eskandari, M. H., & Djafarian, K. (2019) · Clinical Nutrition · doi:10.1016/j.clnu.2018.04.010 · Cited by 534 · see citing works

B-Group vitamin production by lactic acid bacteria - current knowledge and potential applications: Vitamin production by LAB

LeBlanc, J. G., Laiño, J. E., del Valle, M. J., Vannini, V., van Sinderen, D., Taranto, M. P., de Valdez, G. F., de Giori, G. S., & Sesma, F. (2011) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2011.05157.x · Cited by 529 · see citing works

Biogenic Amine Production by Lactic Acid Bacteria: A Review

Barbieri, F., Montanari, C., Gardini, F., & Tabanelli, G. (2019) · Foods · doi:10.3390/foods8010017 · Cited by 528 · see citing works

A randomized synbiotic trial to prevent sepsis among infants in rural India

Panigrahi, P., Parida, S., Nanda, N. C., Satpathy, R., Pradhan, L., Chandel, D. S., Baccaglini, L., Mohapatra, A., Mohapatra, S. S., Misra, P. R., et al. (2017) · Nature · doi:10.1038/nature23480 · Cited by 526 · see citing works

Lactobacillus rhamnosus GG-supplemented formula expands butyrate-producing bacterial strains in food allergic infants

Canani, R. B., Sangwan, N., Stefka, A. T., Nocerino, R., Paparo, L., Aitoro, R., Calignano, A., Khan, A. A., Gilbert, J. A., & Nagler‐Anderson, C. (2015) · The ISME Journal · doi:10.1038/ismej.2015.151 · Cited by 525 · see citing works

Stable Engraftment of Bifidobacterium longum AH1206 in the Human Gut Depends on Individualized Features of the Resident Microbiome

Maldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host &amp; Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517 · see citing works

Accessible, curated metagenomic data through ExperimentHub

Pasolli, E., Schiffer, L., Manghi, P., Renson, A., Obenchain, V., Truong, D. T., Beghini, F., Malik, F., Ramos, M., Dowd, J. B., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4468 · Cited by 514 · see citing works

Increased Proportions of Bifidobacterium and the Lactobacillus Group and Loss of Butyrate-Producing Bacteria in Inflammatory Bowel Disease

Wang, W., Chen, L., Zhou, R., Wang, X., Song, L., Huang, S., Wang, G., & Xia, B. (2014) · Journal of Clinical Microbiology · doi:10.1128/jcm.01500-13 · Cited by 509 · see citing works

Metagenomic species profiling using universal phylogenetic marker genes

Sunagawa, S., Mende, D. R., Zeller, G., Izquierdo-Carrasco, F., Berger, S. A., Kultima, J. R., Coelho, L. P., Arumugam, M., Tap, J., Nielsen, H. B., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2693 · Cited by 503 · see citing works

IMNGS: A comprehensive open resource of processed 16S rRNA microbial profiles for ecology and diversity studies

Lagkouvardos, I., Joseph, D., Kapfhammer, M., Giritli, S., Horn, M., Haller, D., & Clavel, T. (2016) · Scientific Reports · doi:10.1038/srep33721 · Cited by 498 · see citing works

Complete sequence and comparative genome analysis of the dairy bacterium Streptococcus thermophilus

Bolotin, A., Quinquis, B., Renault, P., Sorokin, A., Ehrlich, S. D., Kulakauskas, S., Lapidus, A. L., Goltsman, E., Mazur, M., Pusch, G. D., et al. (2004) · Nature Biotechnology · doi:10.1038/nbt1034 · Cited by 496 · see citing works

Gut microbiota composition and activity in relation to host metabolic phenotype and disease risk

Holmes, E., Li, J. V., Marchesi, J. R., & Nicholson, J. K. (2012) · Cell Metabolism · doi:10.1016/j.cmet.2012.10.007 · Cited by 490 · see citing works

High-Throughput Sequencing and Metagenomics: Moving Forward in the Culture-Independent Analysis of Food Microbial Ecology

Ercolini, D. (2013) · Applied and Environmental Microbiology · doi:10.1128/aem.00256-13 · Cited by 479 · see citing works

Genome-scale analyses of health-promoting bacteria: probiogenomics

Ventura, M., O'Flaherty, S., Claesson, M. J., Turroni, F., Klaenhammer, T. R., van Sinderen, D., & O'Toole, P. W. (2009) · Nature Reviews Microbiology · doi:10.1038/nrmicro2047 · Cited by 471 · see citing works

Randomised clinical trial: the beneficial effects of <scp>VSL</scp>#3 in obese children with non‐alcoholic steatohepatitis

Alisi, A., Bedogni, G., Baviera, G., Giorgio, V., Porro, E., Paris, C., Giammaria, P., Reali, L., Anania, F., & Nobili, V. (2014) · Alimentary Pharmacology &amp; Therapeutics · doi:10.1111/apt.12758 · Cited by 471 · see citing works

An integrated metagenomics pipeline for strain profiling reveals novel patterns of bacterial transmission and biogeography

Nayfach, S., Rodriguez-Mueller, B., Garud, N., & Pollard, K. S. (2016) · Genome Research · doi:10.1101/gr.201863.115 · Cited by 470 · see citing works

Phylogenetic Analysis of the Human Gut Microbiota Using 16S rDNA Clone Libraries and Strictly Anaerobic Culture‐Based Methods

Hayashi, H., Sakamoto, M., & Benno, Y. (2002) · Microbiology and Immunology · doi:10.1111/j.1348-0421.2002.tb02731.x · Cited by 458 · see citing works

Enhanced antiinflammatory capacity of a Lactobacillus plantarum mutant synthesizing modified teichoic acids

Grangette, C., Nutten, S., Palumbo, E., Morath, S., Hermann, C., Dewulf, J., Pot, B., Härtung, T., Pascal Hols, A., & Mercenier, A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504084102 · Cited by 443 · see citing works

Maternal prenatal stress is associated with the infant intestinal microbiota

Zijlmans, M. A. C., Korpela, K., Riksen-Walraven, J. M., de Vos, W. M., & de Weerth, C. (2015) · Psychoneuroendocrinology · doi:10.1016/j.psyneuen.2015.01.006 · Cited by 438 · see citing works

World Gastroenterology Organisation Global Guidelines: Probiotics and Prebiotics October 2011

Guarner, F., Khan, A. G., Garisch, J., Eliakim, R., Gangl, A., Thomson, A., Krabshuis, J., Lemair, T., Kaufmann, P., de Paula, J. A., et al. (2012) · Journal of Clinical Gastroenterology · doi:10.1097/mcg.0b013e3182549092 · Cited by 418 · see citing works

The Lactobacillus and Bifidobacterium microflora of the human intestine: composition and succession.

Reuter, G. (2001) · PubMed · Cited by 417 · see citing works

Ineffectiveness of Lactobacillus johnsonii LA1 for prophylaxis of postoperative recurrence in Crohn’s disease: a randomised, double blind, placebo controlled GETAID trial

Marteau, P. R., Lémann, M., Seksik, P., Laharie, D., Colombel, J. F., Bouhnik, Y., Cadiot, G., Soulé, J. C., Bourreille, A., Metman, E.-H., et al. (2005) · Gut · doi:10.1136/gut.2005.076604 · Cited by 412 · see citing works

Extensive Set of 16S rRNA-Based Probes for Detection of Bacteria in Human Feces

Harmsen, H. J. M., Raangs, G. C., He, T., Degener, J. E., & Welling, G. W. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.6.2982-2990.2002 · Cited by 401 · see citing works

Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis

Hold, G. L., Pryde, S. E., Russell, V. J., Furrie, E., & Flint, H. J. (2002) · FEMS Microbiology Ecology · doi:10.1111/j.1574-6941.2002.tb00904.x · Cited by 401 · see citing works

Assembly: a resource for assembled genomes at NCBI

Kitts, P. A., Church, D. M., Thibaud-Nissen, F., Choi, J., Hem, V., Sapojnikov, V., Smith, R. G., Tatusova, T., Xiang, C., Zherikov, A., et al. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkv1226 · Cited by 398 · see citing works

Clinical application of probiotics in type 2 diabetes mellitus: A randomized, double-blind, placebo-controlled study

Tonucci, L. B., dos Santos, K. M. O., de Oliveira, L. L., Ribeiro, S. M. R., & Martino, H. S. D. (2015) · Clinical Nutrition · doi:10.1016/j.clnu.2015.11.011 · Cited by 389 · see citing works

Discovering probiotic microorganisms: in vitro, in vivo, genetic and omics approaches

Papadimitriou, K., Ζουμποπούλου, Γ., Foligné, B., Alexandraki, V., Κάζου, Μ., Pot, B., & Tsakalidou, E. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00058 · Cited by 388 · see citing works

Functional Analysis of Lactobacillus rhamnosus GG Pili in Relation to Adhesion and Immunomodulatory Interactions with Intestinal Epithelial Cells

Lebeer, S., Claes, I. J. J., Tytgat, H. L. P., Verhoeven, T. L. A., Marien, E., von Ossowski, I., Reunanen, J., Palva, A., de Vos, W. M., Keersmaecker, S. C. J. D., et al. (2011) · Applied and Environmental Microbiology · doi:10.1128/aem.06192-11 · Cited by 378 · see citing works

Strain-level microbial epidemiology and population genomics from shotgun metagenomics

Scholz, M., Ward, D. V., Pasolli, E., Tolio, T., Zolfo, M., Asnicar, F., Truong, D. T., Tett, A., Morrow, A. L., & Segata, N. (2016) · Nature Methods · doi:10.1038/nmeth.3802 · Cited by 374 · see citing works

Production, Properties, and Industrial Food Application of Lactic Acid Bacteria-Derived Exopolysaccharides

Zannini, E., Waters, D. M., Coffey, A., & Arendt, E. K. (2016) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-015-7172-2 · Cited by 371 · see citing works

Dairy consumption and risk of type 2 diabetes: 3 cohorts of US adults and an updated meta-analysis

Chen, M., Sun, Q., Giovannucci, E., Mozaffarian, D., Manson, J. E., Willett, W. C., & Hu, F. B. (2014) · BMC Medicine · doi:10.1186/s12916-014-0215-1 · Cited by 370 · see citing works

Intestinal Lactobacillus in health and disease, a driver or just along for the ride?

Heeney, D. D., Gareau, M. G., & Marco, M. L. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.08.004 · Cited by 367 · see citing works

Large-scale genome-wide analysis links lactic acid bacteria from food with the gut microbiome

Pasolli, E., De Filippis, F., Mauriello, I. E., Cumbo, F., Walsh, A. M., Leech, J., Cotter, P. D., Segata, N., & Ercolini, D. (2020) · Nature Communications · doi:10.1038/s41467-020-16438-8 · Cited by 367 · see citing works

Fermentation-enabled wellness foods: A fresh perspective

Xiang, H., Sun‐Waterhouse, D., Waterhouse, G. I. N., Cui, C., & Ruan, Z. (2019) · Food Science and Human Wellness · doi:10.1016/j.fshw.2019.08.003 · Cited by 364 · see citing works

Bacterial Neuroactive Compounds Produced by Psychobiotics

Wall, R., Cryan, J. F., Ross, R. P., Fitzgerald, G. F., Dinan, T. G., & Stanton, C. (2014) · Advances in experimental medicine and biology · doi:10.1007/978-1-4939-0897-4_10 · Cited by 362 · see citing works

Molecular analysis of jejunal, ileal, caecal and recto-sigmoidal human colonic microbiota using 16S rRNA gene libraries and terminal restriction fragment length polymorphism

Hayashi, H., Takahashi, R., Nishi, T., Sakamoto, M., & Benno, Y. (2005) · Journal of Medical Microbiology · doi:10.1099/jmm.0.45935-0 · Cited by 360 · see citing works

Genus-Wide Assessment of Antibiotic Resistance in <i>Lactobacillus</i> spp

Campedelli, I., Mathur, H., Salvetti, E., Clarke, S., Rea, M. C., Torriani, S., Ross, R. P., Hill, C., & O’Toole, P. W. (2019) · Applied and Environmental Microbiology · doi:10.1128/aem.01738-18 · Cited by 343 · see citing works

Lactobacillus reuteri DSM 17938 in Infantile Colic: A Randomized, Double-Blind, Placebo-Controlled Trial

Savino, F., Cordisco, L., Tarasco, V., Palumeri, E., Calabrese, R., Oggero, R., Roos, S., & Matteuzzi, D. (2010) · PEDIATRICS · doi:10.1542/peds.2010-0433 · Cited by 342 · see citing works

Probiotic VSL#3 Reduces Liver Disease Severity and Hospitalization in Patients With Cirrhosis: A Randomized, Controlled Trial

Dhiman, R. K., Rana, B., Agrawal, S., Garg, A., Chopra, M., Thumburu, K. K., Khattri, A., Malhotra, S., Duseja, A., & Chawla, Y. K. (2014) · Gastroenterology · doi:10.1053/j.gastro.2014.08.031 · Cited by 339 · see citing works

Lactic acid bacteria and bifidobacteria with potential to design natural biofunctional health-promoting dairy foods

Linares, D. M., Gómez, C., Renes, E., Fresno, J. M., Tornadijo, M. E., Ross, R. P., & Stanton, C. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.00846 · Cited by 335 · see citing works

Bioactive Molecules Released in Food by Lactic Acid Bacteria: Encrypted Peptides and Biogenic Amines

Pessione, E., & Cirrincione, S. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.00876 · Cited by 333 · cited 3× · see citing works

Aberrant gut microbiota composition at the onset of type 1 diabetes in young children

de Goffau, M. C., Fuentes, S., van den Bogert, B., Honkanen, H., de Vos, W. M., Welling, G. W., Hyöty, H., & Harmsen, H. J. M. (2014) · Diabetologia · doi:10.1007/s00125-014-3274-0 · Cited by 328 · see citing works

<i>Lactobacillus reuteri</i> reduces bone loss in older women with low bone mineral density: a randomized, placebo‐controlled, double‐blind, clinical trial

Nilsson, A. G., Sundh, D., Bäckhed, F., & Lorentzon, M. (2018) · Journal of Internal Medicine · doi:10.1111/joim.12805 · Cited by 323 · see citing works

Yogurt and other fermented foods as sources of health-promoting bactéria

Kok, C. R., & Hutkins, R. (2018) · Nutrition Reviews · doi:10.1093/nutrit/nuy056 · Cited by 317 · see citing works

Probiotic supplementation improves inflammatory status in patients with rheumatoid arthritis

Vaghef‐Mehrabany, E., Alipour, B., Rad, A. H., Sharif, S., Jafarabadi, M. A., & Zavvari, S. (2013) · Nutrition · doi:10.1016/j.nut.2013.09.007 · Cited by 312 · see citing works

Lactic acid bacteria secrete metabolites retaining anti-inflammatory properties after intestinal transport

Ménard, S., Candalh, C., Bambou, J. C., Terpend, K., Cerf–Bensussan, N., & Heyman, M. (2004) · Gut · doi:10.1136/gut.2003.026252 · Cited by 309 · see citing works

Effect of Probiotic (VSL#3) and Omega-3 on Lipid Profile, Insulin Sensitivity, Inflammatory Markers, and Gut Colonization in Overweight Adults: A Randomized, Controlled Trial

Rajkumar, H., Mahmood, N., Kumar, M., Varikuti, S. R., Challa, H. R., & Myakala, S. P. (2014) · Mediators of Inflammation · doi:10.1155/2014/348959 · Cited by 301 · see citing works

Multicenter randomized-controlled clinical trial of probiotics (Lactobacillus johnsonii, LA1) on early endoscopic recurrence of Crohnʼs disease after ileo-caecal resection

Gossum, A. V., Dewit, O., Louis, E. J., Hertogh, G., Baert, F., Fontaine, F., Devos, M., Enslen, M., Paintin, M., & Franchimont, D. P. (2006) · Inflammatory Bowel Diseases · doi:10.1002/ibd.20063 · Cited by 296 · see citing works

Phenotypic and genomic diversity of Lactobacillus plantarum strains isolated from various environmental niches

Siezen, R. J., Tzeneva, V. A., Castioni, A., Wels, M., Phan, H. T. K., Rademaker, J. L. W., Starrenburg, M. J. C., Kleerebezem, M., Douwe Molenaar, B., & Vlieg, J. E. T. V. H. (2009) · Environmental Microbiology · doi:10.1111/j.1462-2920.2009.02119.x · Cited by 293 · see citing works

Health Benefits of Lactobacillus gasseri CP2305 Tablets in Young Adults Exposed to Chronic Stress: A Randomized, Double-Blind, Placebo-Controlled Study

Nishida, K., Sawada, D., Kuwano, Y., Tanaka, H., & Rokutan, K. (2019) · Nutrients · doi:10.3390/nu11081859 · Cited by 292 · see citing works

Fermented Milk Containing Lactobacillus casei Strain Shirota Preserves the Diversity of the Gut Microbiota and Relieves Abdominal Dysfunction in Healthy Medical Students Exposed to Academic Stress

Kato-Kataoka, A., Nishida, K., Takada, M., Kawai, M., Kikuchi-Hayakawa, H., Suda, K., Ishikawa, H., Gondo, Y., Shimizu, K., Matsuki, T., et al. (2016) · Applied and Environmental Microbiology · doi:10.1128/aem.04134-15 · Cited by 288 · see citing works

Alterations in Intestinal Microbiota Correlate With Susceptibility to Type 1 Diabetes

Alkanani, A. K., Hara, N., Gottlieb, P. A., Ir, D., Robertson, C. E., Wagner, B. D., Frank, D. N., & Zipris, D. (2015) · Diabetes · doi:10.2337/db14-1847 · Cited by 287 · see citing works

Interactions of Surface Exopolysaccharides from Bifidobacterium and Lactobacillus within the Intestinal Environment

Castro-Bravo, N., Wells, J. M., Margolles, A., & Ruas-Madiedo, P. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02426 · Cited by 284 · see citing works

Establishing What Constitutes a Healthy Human Gut Microbiome: State of the Science, Regulatory Considerations, and Future Directions

McBurney, M. I., Davis, C. D., Fraser, C. M., Schneeman, B. O., Huttenhower, C., Verbeke, K., Walter, J., & Latulippe, M. E. (2019) · Journal of Nutrition · doi:10.1093/jn/nxz154 · Cited by 283 · see citing works

Menaquinones, Bacteria, and the Food Supply: The Relevance of Dairy and Fermented Food Products to Vitamin K Requirements

Walther, B., Karl, J. P., Booth, S. L., & Boyaval, P. (2013) · Advances in Nutrition · doi:10.3945/an.113.003855 · Cited by 271 · see citing works

Probiotic Supplementation in Patients with Alzheimer’s Dementia - An Explorative Intervention Study

Leblhuber, F., Steiner, K., Schuetz, B., Fuchs, D., & Gostner, J. M. (2018) · Current Alzheimer Research · doi:10.2174/1389200219666180813144834 · Cited by 269 · see citing works

Metabolic effects of L actobacillus reuteri DSM 17938 in people with type 2 diabetes: A randomized controlled trial

Mobini, R., Tremaroli, V., Ståhlman, M., Karlsson, F. H., Levin, M., Ljungberg, M., Sohlin, M. C., Forslund, H. B., Perkins, R., Bäckhed, F., et al. (2016) · Diabetes Obesity and Metabolism · doi:10.1111/dom.12861 · Cited by 266 · see citing works

Ecological robustness of the gut microbiota in response to ingestion of transient food-borne microbes

Zhang, C., Derrien, M., Levenez, F., Brazeilles, R., Ballal, S. A., Kim, J., Degivry, M.-C., Quéré, G., Garault, P., van Hylckama Vlieg, J. E. T., et al. (2016) · The ISME Journal · doi:10.1038/ismej.2016.13 · Cited by 264 · see citing works

Effects of Lactobacillus plantarum PS128 on Children with Autism Spectrum Disorder in Taiwan: A Randomized, Double-Blind, Placebo-Controlled Trial

Liu, Y.-W., Liong, M., Chung, Y.-C. E., Huang, H.-Y., Peng, W.-S., Cheng, Y.-F., Lin, Y.-S., Wu, Y., & Tsai, Y.-C. (2019) · Nutrients · doi:10.3390/nu11040820 · Cited by 264 · see citing works

Inclusion of Fermented Foods in Food Guides around the World

Chilton, S., Burton, J. P., & Reid, G. (2015) · Nutrients · doi:10.3390/nu7010390 · Cited by 262 · see citing works

Metagenomics insights into food fermentations

Filippis, F. D., Parente, E., & Ercolini, D. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12421 · Cited by 257 · see citing works

Gut feelings: a randomised, triple-blind, placebo-controlled trial of probiotics for depressive symptoms

Chahwan, B., Kwan, S., Isik, A., van Hemert, S., Burke, C., & Roberts, L. (2019) · Journal of Affective Disorders · doi:10.1016/j.jad.2019.04.097 · Cited by 256 · see citing works

A Multi-strain Probiotic Reduces the Fatty Liver Index, Cytokines and Aminotransferase levels in NAFLD Patients: Evidence from a Randomized Clinical Trial

Kobyliak, N. M., Abenavoli, L., Mykhalchyshyn, G., Kononenko, L., Boccuto, L., Kyriienko, D., & Dynnyk, O. (2018) · Journal of Gastrointestinal and Liver Diseases · doi:10.15403/jgld.2014.1121.271.kby · Cited by 256 · see citing works

Effect of the consumption of a new symbiotic shake on glycemia and cholesterol levels in elderly people with type 2 diabetes mellitus

Moroti, C., Magri, L. F. S., Costa, M. D. R., Cavallini, D., & Sivieri, K. (2012) · Lipids in Health and Disease · doi:10.1186/1476-511x-11-29 · Cited by 254 · see citing works

Altered molecular signature of intestinal microbiota in irritable bowel syndrome patients compared with healthy controls: A systematic review and meta-analysis

Liu, H.-N., Wu, H., Chen, Y.-Z., Chen, Y.-J., Shen, X.-Z., & Liu, T.-T. (2017) · Digestive and Liver Disease · doi:10.1016/j.dld.2017.01.142 · Cited by 254 · see citing works

Shared mechanisms among probiotic taxa: implications for general probiotic claims

Sanders, M. E., Benson, A. K., Lebeer, S., Merenstein, D. J., & Klaenhammer, T. R. (2017) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2017.09.007 · Cited by 254 · see citing works

Taking it Personally: Personalized Utilization of the Human Microbiome in Health and Disease

Zmora, N., Zeevi, D., Korem, T., Segal, E., & Elinav, E. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2015.12.016 · Cited by 252 · see citing works

Treating infant colic with the probiotic Lactobacillus reuteri: double blind, placebo controlled randomised trial

Sung, V., Hiscock, H., Tang, M. L. K., Mensah, F. K., Nation, M. L., Satzke, C., Heine, R. G., Stock, A., Barr, R. G., & Wake, M. A. (2014) · BMJ · doi:10.1136/bmj.g2107 · Cited by 249 · see citing works

Nomadic lifestyle of Lactobacillus plantarum revealed by comparative genomics of 54 strains isolated from different habitats

Martino, M. E., Bayjanov, J. R., Caffrey, B. E., Wels, M., Joncour, P., Hughes, S., Gillet, B., Kleerebezem, M., van Hijum, S. A. F. T., & Leulier, F. (2016) · Environmental Microbiology · doi:10.1111/1462-2920.13455 · Cited by 245 · see citing works

The small intestine microbiota, nutritional modulation and relevance for health

El Aidy, S., van den Bogert, B., & Kleerebezem, M. (2015) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2014.09.005 · Cited by 244 · see citing works

A Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology

Zheng, J., Ruan, L., Sun, M., & Gänzle, M. G. (2015) · Applied and Environmental Microbiology · doi:10.1128/aem.02116-15 · Cited by 236 · see citing works

Community genomics in microbial ecology and evolution

Allen, E. E., & Banfield, J. F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1157 · Cited by 234 · see citing works

Modulation of Fecal Clostridiales Bacteria and Butyrate by Probiotic Intervention with Lactobacillus paracasei DG Varies among Healthy Adults

Ferrario, C., Taverniti, V., Milani, C., Fiore, W., Laureati, M., De Noni, I., Stuknyte, M., Chouaia, B., Riso, P., & Guglielmetti, S. (2014) · The Journal of Nutrition · doi:10.3945/jn.114.197723 · Cited by 228 · see citing works

The Human Gastrointestinal Tract

MITSUOKA, T. (1992) · Springer eBooks · doi:10.1007/978-1-4615-3522-5_4 · Cited by 225 · see citing works

The amount and type of dairy product intake and incident type 2 diabetes: results from the EPIC-InterAct Study

Sluijs, I., Forouhi, N. G., Beulens, J. W., van der Schouw, Y. T., Agnoli, C., Arriola, L., Balkau, B., Barricarte, A., Boeing, H., Bueno-de-Mesquita, H. B., et al. (2012) · The American Journal of Clinical Nutrition · doi:10.3945/ajcn.111.021907 · Cited by 223 · see citing works

Effect of multi-strain probiotics (multi-strain microbial cell preparation) on glycemic control and other diabetes-related outcomes in people with type 2 diabetes: a randomized controlled trial

Firouzi, S., Majid, H. A., Ismail, A., Kamaruddin, N. A., & Yusof, B. N. M. (2016) · European Journal of Nutrition · doi:10.1007/s00394-016-1199-8 · Cited by 220 · see citing works

Exopolysaccharides from Sourdough Lactic Acid Bacteria

Galle, S., & Arendt, E. K. (2013) · Critical Reviews in Food Science and Nutrition · doi:10.1080/10408398.2011.617474 · Cited by 219 · see citing works

Role of lactic acid bacteria (LAB) in food preservation and human health—A review

Soomro, A. H., Masud, T., & Anwaar, K. (2001) · Pakistan Journal of Nutrition · doi:10.3923/pjn.2002.20.24 · Cited by 219 · see citing works

Lactobacillus plantarum 299v Supplementation Improves Vascular Endothelial Function and Reduces Inflammatory Biomarkers in Men With Stable Coronary Artery Disease

Malik, M. A., Suboc, T. M. B., Tyagi, S., Salzman, N. H., Wang, J., Ying, R., Tanner, M. J., Kakarla, M., Baker, J. E., & Widlansky, M. E. (2018) · Circulation Research · doi:10.1161/circresaha.118.313565 · Cited by 218 · see citing works

Disrupted Intestinal Microbiota and Intestinal Inflammation in Children with Cystic Fibrosis and Its Restoration with Lactobacillus GG: A Randomised Clinical Trial

Bruzzese, E., Callegari, M. L., Raia, V., Viscovo, S., Scotto, R., Ferrari, S., Morelli, L., Buccigrossi, V., Vecchio, A. L., Ruberto, E., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0087796 · Cited by 217 · see citing works

Correlation between body mass index and faecal microbiota from children

Ignácio, A., Fernandes, M. R., Rodrigues, V. A. A., Groppo, F. C., Cardoso, A. L., Ávila-Campos, M. J., & Nakano, V. (2015) · Clinical Microbiology and Infection · doi:10.1016/j.cmi.2015.10.031 · Cited by 204 · see citing works

Consumption of fermented foods is associated with systematic differences in the gut microbiome and metabolome

Taylor, B. C., Lejzerowicz, F., Poirel, M., Shaffer, J. P., Jiang, L., Aksenov, A., Litwin, N., Humphrey, G., Martino, C., Miller-Montgomery, S., et al. (2020) · mSystems · doi:10.1128/msystems.00901-19 · Cited by 203 · see citing works

Effect of alive probiotic on insulin resistance in type 2 diabetes patients: Randomized clinical trial

Kobyliak, N. M., Falalyeyeva, T. M., Mykhalchyshyn, G., Kyriienko, D., & Komisarenko, I. (2018) · Diabetes & Metabolic Syndrome Clinical Research & Reviews · doi:10.1016/j.dsx.2018.04.015 · Cited by 198 · see citing works

Occurrence and Dynamism of Lactic Acid Bacteria in Distinct Ecological Niches: A Multifaceted Functional Health Perspective

George, F., Daniel, C., Thomas, M., Singer, E., Guilbaud, A., Tessier, F. J., Revol-Junelles, A.-M., Borges, F., & Foligné, B. (2018) · Frontiers in Microbiology · doi:10.3389/fmicb.2018.02899 · Cited by 198 · see citing works

Associations between the human intestinal microbiota, Lactobacillus rhamnosus GG and serum lipids indicated by integrated analysis of high-throughput profiling data

Lahti, L., Salonen, A., Kekkonen, R. A., Salojärvi, J., Jalanka, J., Palva, A., Orešič, M., & de Vos, W. M. (2013) · PeerJ · doi:10.7717/peerj.32 · Cited by 196 · see citing works

Metatranscriptomics reveals temperature-driven functional changes in microbiome impacting cheese maturation rate.

De Filippis, F., Genovese, A., Ferranti, P., Gilbert, J. A., & Ercolini, D. (2016) · Scientific Reports · doi:10.1038/srep21871 · Cited by 196 · see citing works

Yogurt consumption and risk of colorectal cancer in the Italian European prospective investigation into cancer and nutrition cohort

Pala, V. M., Sieri, S., Berrino, F., Vineis, P., Sacerdote, C., Palli, D., Masala, G., Panico, S., Mattiello, A., Tumino, R., et al. (2011) · International Journal of Cancer · doi:10.1002/ijc.26193 · Cited by 191 · see citing works

Alterations of gut microbiota in patients with irritable bowel syndrome: A systematic review and meta‐analysis

Zhuang, X., Xiong, L., Li, L., Li, M., & Chen, M. (2016) · Journal of Gastroenterology and Hepatology · doi:10.1111/jgh.13471 · Cited by 191 · see citing works

Beneficial metabolic effects of selected probiotics on diet‐induced obesity and insulin resistance in mice are associated with improvement of dysbiotic gut microbiota

Alard, J., Lehrter, V., Rhimi, M., Mangin, I., Peucelle, V., Abraham, A., Mariadassou, M., Maguin, E., Waligora‐Dupriet, A., Pot, B., et al. (2015) · Environmental Microbiology · doi:10.1111/1462-2920.13181 · Cited by 190 · see citing works

One health, fermented foods and gut microbiota

Bell, V., Ferrão, J., Pimentel, L., Pintado, M., & Fernandes, T. (2018) · Foods · doi:10.3390/foods7120195 · Cited by 188 · see citing works

Probiotics for the Prevention of Gestational Diabetes Mellitus in Overweight and Obese Women: Findings From the SPRING Double-Blind Randomized Controlled Trial

Callaway, L. K., McIntyre, H. D., Barrett, H. L., Foxcroft, K., Tremellen, A., Lingwood, B. E., Tobin, J. M., Wilkinson, S., Kothari, A., Morrison, M., et al. (2019) · Diabetes Care · doi:10.2337/dc18-2248 · Cited by 187 · see citing works

Fermented kimchi reduces body weight and improves metabolic parameters in overweight and obese patients

Kim, E. K., An, S.-Y., Lee, M.-S., Kim, T. H., Lee, H.-K., Hwang, W. S., Choe, S. J., Kim, T., Han, S. J., Kim, H. J., et al. (2011) · Nutrition Research · doi:10.1016/j.nutres.2011.05.011 · Cited by 184 · see citing works

Transient invaders can induce shifts between alternative stable states of microbial communities

Amor, D. R., Ratzke, C., & Gore, J. (2020) · Science Advances · doi:10.1126/sciadv.aay8676 · Cited by 184 · see citing works

Composition and function of sourdough microbiota: From ecological theory to bread quality

Gänzle, M. G., & Ripari, V. (2016) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2016.05.004 · Cited by 183 · see citing works

Comparative Genome Analysis of Lactococcus lactis Indicates Niche Adaptation and Resolves Genotype/Phenotype Disparity

Wels, M., Siezen, R., van Hijum, S., Kelly, W. J., & Bachmann, H. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00004 · Cited by 181 · see citing works

Non-dairy lactic fermentations: the cereal world

Vogel, R. F., Knorr, R., Müller, M. R. A., Steudel, U., Gänzle, M. G., & Ehrmann, M. A. (1999) · Springer eBooks · doi:10.1007/978-94-017-2027-4_27 · Cited by 180 · see citing works

Fermented foods, the gut and mental health: a mechanistic overview with implications for depression and anxiety

Aslam, H., Green, J., Jacka, F. N., Collier, F., Berk, M., Pasco, J., & Dawson, S. L. (2020) · Nutritional Neuroscience · doi:10.1080/1028415x.2018.1544332 · Cited by 179 · see citing works

Genome Sequence and Comparative Genome Analysis of Lactobacillus casei: Insights into Their Niche-Associated Evolution

Cai, H., Thompson, R. M., Budinich, M., Broadbent, J. R., & Steele, J. L. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp019 · Cited by 177 · see citing works

Effect of daily consumption of probiotic yoghurt on insulin resistance in pregnant women: a randomized controlled trial

Asemi, Z., Samimi, M., Tabassi, Z., Rad, M. N., Foroushani, A. R., Khorammian, H., & Esmaillzadeh, A. (2012) · European Journal of Clinical Nutrition · doi:10.1038/ejcn.2012.189 · Cited by 175 · see citing works

The intestinal LABs.

Vaughan, E. E., de Vries, M. C., Zoetendal, E. G., Amor, K. B., Akkermans, A. D. L., & de Vos, W. M. (2002) · PubMed · Cited by 175 · see citing works

DESMAN: a new tool for de novo extraction of strains from metagenomes

Quince, C., Delmont, T., Raguideau, S., Alneberg, J., Darling, A., Collins, G., & Eren, A. (2017) · Genome Biology · doi:10.1186/s13059-017-1309-9 · Cited by 175 · see citing works

Unexplored microbial diversity from 2,500 food metagenomes and links with the human microbiome.

Carlino, N., Blanco-Míguez, A., Punčochář, M., Mengoni, C., Pinto, F., Tatti, A., Manghi, P., Armanini, F., Avagliano, M., Barcenilla, C., et al. (2024) · Cell · doi:10.1016/j.cell.2024.07.039 · Cited by 146 · see citing works

Unlocking the Potential of Probiotics: A Comprehensive Review on Research, Production, and Regulation of Probiotics

da Silva, T. F., Glória, R. D. A., Americo, M. F., Freitas, A. D. S., de Jesus, L. C. L., Barroso, F. A. L., Laguna, J. G., Coelho-Rocha, N. D., Tavares, L. M., le Loir, Y., et al. (2024) · Probiotics and Antimicrobial Proteins · doi:10.1007/s12602-024-10247-x · Cited by 117 · see citing works

Deciphering the gut microbiome: The revolution of artificial intelligence in microbiota analysis and intervention

Abavisani, M., Khoshrou, A., Foroushan, S. K., Ebadpour, N., & Sahebkar, A. (2024) · Current Research in Biotechnology · doi:10.1016/j.crbiot.2024.100211 · Cited by 75 · see citing works

Lactic acid bacteria in cow raw milk for cheese production: Which and how many?

Bettera, L., Levante, A., Bancalari, E., Bottari, B., & Gatti, M. (2023) · Frontiers in microbiology · doi:10.3389/fmicb.2022.1092224 · Cited by 47 · see citing works

The Interrelationship Between Microbiota and Peptides During Ripening as a Driver for Parmigiano Reggiano Cheese Quality

Bottari, B., Levante, A., Bancalari, E., Sforza, S., Bottesini, C., Prandi, B., De Filippis, F., Ercolini, D., Nocetti, M., & Gatti, M. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.581658 · Cited by 41 · see citing works

Whole Genome Sequencing and Extracellular Metabolite Profiling of Lactiplantibacillus plantarum FRT4: Insights into Probiotic Functionality

Huang, Y., Meng, K., Liu, G., Chen, Z., Han, Y., Yang, P., Zhang, R., & Cai, H. (2025) · Biology · doi:10.3390/biology14091167 · Cited by 7 · see citing works

Vitamins for the Gut Microbiome

Steinert, R. E., Lee, Y. K., & Sybesma, W. (2019) · Trends in Molecular Medicine · doi:10.1016/j.molmed.2019.11.005 · Cited by 115 · see citing works

Microbiome-based stratification to guide dietary interventions to improve human health

Liu, Z., de Vries, B., Gerritsen, J., Smidt, H., & Zoetendal, E. G. (2020) · Nutrition Research · doi:10.1016/j.nutres.2020.07.004 · Cited by 42 · see citing works

A Microbiome Restoration Strategy Modulates the Gut Microbiome and Metabolic Markers in Healthy Adults

Li, F. (2021) · doi:10.52843/cassyni.wk4b29

Gut-on-chip for ecological and causal human gut microbiome research

Moossavi, S., Arrieta, M., Sanati‐Nezhad, A., & Bishehsari, F. (2022) · Trends in Microbiology · doi:10.1016/j.tim.2022.01.014 · Cited by 52 · see citing works

Vegetarian Diets and the Microbiome

Orlich, M. J., Segovia‐Siapco, G., & Jung, S. M. (2017) · Elsevier eBooks · doi:10.1016/b978-0-12-803968-7.00024-1 · Cited by 8 · see citing works