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

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

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 19,549

Prokka: rapid prokaryotic genome annotation

Seemann, T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu153 · Cited by 18,937

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

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

Structure, function and diversity of the healthy human microbiome

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

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

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 10,133

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

Untitled work

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

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

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

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

Changes of Intestinal Functions in Liver Cirrhosis

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

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

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

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

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

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 5,144

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

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

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

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

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 4,480

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

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

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 3,614

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

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

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

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 2,978

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

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 2,815

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

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

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

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

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

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

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

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

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

Guidelines for the evaluation of probiotics in food

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

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

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

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

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×

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

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

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

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

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

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

Human gut microbiome: Hopes, threats and promises

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

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

Scopus database: a review

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

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

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

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

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 1,161

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

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

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 1,048

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 1,031

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

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

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

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

Bacteriocin production as a mechanism for the antiinfective activity of Lactobacillus salivarius 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

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

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 & Microbe · doi:10.1016/j.chom.2012.10.012 · Cited by 836

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 & Microbe · doi:10.1016/j.chom.2015.09.008 · Cited by 823

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

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×

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

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

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

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

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

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 737

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

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

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

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

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

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

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

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 639

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 611

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 606

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

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 601

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

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 574

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

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 567

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

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

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

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

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 538

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

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

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

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

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 524

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 & Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517

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

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

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 507

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

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

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

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

Randomised clinical trial: the beneficial effects of VSL#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 & Therapeutics · doi:10.1111/apt.12758 · Cited by 471

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

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

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

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

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

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

Reuter, G. (2001) · PubMed · Cited by 416

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 413

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

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 406

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 402

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

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 400

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

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 389

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 377

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 373

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

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

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

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

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

Genus-Wide Assessment of Antibiotic Resistance in Lactobacillus 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

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

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

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

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×

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 333

Lactobacillus reuteri 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

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 321

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

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

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 305

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

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

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 296

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 294

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

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

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

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 272

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

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 271

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

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 265

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

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 264

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

Metagenomics insights into food fermentations

Filippis, F. D., Parente, E., & Ercolini, D. (2016) · Microbial Biotechnology · doi:10.1111/1751-7915.12421 · Cited by 262

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 260

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 258

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

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

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

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

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

Community genomics in microbial ecology and evolution

Allen, E. E., & Banfield, J. F. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1157 · Cited by 243

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

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 230

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

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 227

The Human Gastrointestinal Tract

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

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

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

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

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

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 203

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

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 202

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 201

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 198

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

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

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 195

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 193

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

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

Quince, C., Connelly, S., Raguideau, S., Alneberg, J., Shin, S. G., Collins, G., & Eren, A. M. (2017) · Genome biology · doi:10.1186/s13059-017-1309-9 · Cited by 191

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

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

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 186

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

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 181

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

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

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 180

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

Consumption of Yogurt, Low-Fat Milk, and Other Low-Fat Dairy Products Is Associated with Lower Risk of Metabolic Syndrome Incidence in an Elderly Mediterranean Population

Babió, N., Becerra‐Tomás, N., Martínez‐González, M. Á., Corella, D., Estruch, R., Ros, E., Sayón-Orea, C., Fitó, M., Serra‐Majem, L., Arós, F., et al. (2015) · Journal of Nutrition · doi:10.3945/jn.115.214593 · Cited by 176

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

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

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

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

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

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

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 43

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 54

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