Bifidobacteriaceae diversity in the human microbiome from a large-scale genome-wide analysis

Basic local alignment search tool

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990) · Journal of Molecular Biology · doi:10.1006/jmbi.1990.9999 · Cited by 98,669 · see citing works

Fast gapped-read alignment with Bowtie 2

Langmead, B., & Salzberg, S. L. (2012) · Nature Methods · doi:10.1038/nmeth.1923 · Cited by 56,400 · see citing works

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

Katoh, K., & Standley, D. M. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst010 · Cited by 46,209 · see citing works

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

Stamatakis, A. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu033 · Cited by 32,291 · see citing works

Prokka: rapid prokaryotic genome annotation

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009490 · Cited by 14,894 · see citing works

Fast and sensitive protein alignment using DIAMOND

Buchfink, B., Xie, C., & Huson, D. H. (2015) · Nature Methods · doi:10.1038/nmeth.3176 · Cited by 14,201 · 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

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

Capella-Gutiérrez, S., Silla-Martinez, J., & Gabaldón, T. (2009) · Bioinform. · doi:10.1093/bioinformatics/btp348 · Cited by 12,052 · 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

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

Letunić, I., & Peer Bork, B. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz239 · Cited by 5,988 · see citing works

Mash: fast genome and metagenome distance estimation using MinHash

(2016) · Genome biology · doi:10.1186/s13059-016-0997-x · Cited by 3,373 · see citing works

Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea

The Genome Standards Consortium, Bowers, R. M., Kyrpides, N. C., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3893 · Cited by 2,624 · see citing works

Integrating taxonomic, functional, and strain-level profiling of diverse microbial communities with bioBakery 3

Beghini, F., McIver, L. J., Blanco-Míguez, A., Dubois, L., Asnicar, F., Maharjan, S., Mailyan, A., Manghi, P., Scholz, M., Thomas, A. M., et al. (2021) · eLife · doi:10.7554/elife.65088 · Cited by 2,303 · see citing works

dbCAN2: a meta server for automated carbohydrate-active enzyme annotation

Zhang, H., Yohe, T., Huang, L., Entwistle, S., Wu, P., Yang, Z., Busk, P. K., Xu, Y., & Yin, Y. (2018) · Nucleic Acids Research · doi:10.1093/nar/gky418 · Cited by 2,224 · see citing works

MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities

(2015) · doi:10.7717/peerj.1165 · Cited by 1,960 · 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

Age-related changes in gut microbiota composition from newborn to centenarian: a cross-sectional study

Odamaki, T., Kato, K., Sugahara, H., Hashikura, N., Takahashi, S., Xiao, J.-Z., Abe, F., & Osawa, R. (2016) · BMC Microbiology · doi:10.1186/s12866-016-0708-5 · Cited by 1,521 · see citing works

A unified catalog of 204,938 reference genomes from the human gut microbiome

Almeida, A., Nayfach, S., Boland, M., Strozzi, F., Beracochea, M., Shi, Z. J., Pollard, K. S., Sakharova, E., Parks, D. H., Hugenholtz, P., et al. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0603-3 · Cited by 1,367 · see citing works

Mother-to-Infant Microbial Transmission from Different Body Sites Shapes the Developing Infant Gut Microbiome

Ferretti, P., Pasolli, E., Tett, A., Asnicar, F., Gorfer, V., Fedi, S., Armanini, F., Truong, D. T., Manara, S., Zolfo, M., et al. (2018) · Cell Host & Microbe · doi:10.1016/j.chom.2018.06.005 · Cited by 1,292 · see citing works

The anxiolytic effect of Bifidobacterium longum NCC3001 involves vagal pathways for gut-brain communication

Bercik, P., Park, A. J., Sinclair, D., Khoshdel, A., Lu, J., Huang, X., Deng, Y., Blennerhassett, P. A., Fahnestock, M., Moine, D., et al. (2011) · Neurogastroenterology & Motility · doi:10.1111/j.1365-2982.2011.01796.x · Cited by 1,018 · see citing works

Precise phylogenetic analysis of microbial isolates and genomes from metagenomes using PhyloPhlAn 3.0

Asnicar, F., Thomas, A. M., Beghini, F., Mengoni, C., Manara, S., Manghi, P., Zhu, Q., Bolzan, M., Cumbo, F., May, U., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16366-7 · Cited by 869 · see citing works

Molecular Monitoring of Succession of Bacterial Communities in Human Neonates

Favier, C. F., Vaughan, E. E., de Vos, W. M., & Akkermans, A. D. L. (2002) · Applied and Environmental Microbiology · doi:10.1128/aem.68.1.219-226.2002 · Cited by 859 · see citing works

Gut Bifidobacteria Populations in Human Health and Aging

Arboleya, S., Watkins, C., Stanton, C., & Ross, R. P. (2016) · Frontiers in Microbiology · doi:10.3389/fmicb.2016.01204 · Cited by 683 · see citing works

Machine Learning Meta-analysis of Large Metagenomic Datasets: Tools and Biological Insights

Pasolli, E., Truong, D. T., Malik, F., Waldron, L., & Segata, N. (2016) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1004977 · Cited by 659 · see citing works

Intestinal microbiota in health and disease: Role of bifidobacteria in gut homeostasis

Tojo, R. (2014) · World Journal of Gastroenterology · doi:10.3748/wjg.v20.i41.15163 · Cited by 533 · 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

The Prevotella copri Complex Comprises Four Distinct Clades Underrepresented in Westernized Populations

Tett, A., Huang, K. D., Asnicar, F., Fehlner-Peach, H., Pasolli, E., Karcher, N., Armanini, F., Manghi, P., Bonham, K., Zolfo, M., et al. (2019) · Cell Host & Microbe · doi:10.1016/j.chom.2019.08.018 · Cited by 476 · see citing works

The person-to-person transmission landscape of the gut and oral microbiomes

Valles-Colomer, M., Blanco-Míguez, A., Manghi, P., Asnicar, F., Dubois, L., Golzato, D., Armanini, F., Cumbo, F., Huang, K. D., Manara, S., et al. (2023) · Nature · doi:10.1038/s41586-022-05620-1 · Cited by 449 · see citing works

Bifidobacteria and their role in human health

MITSUOKA, T. (1990) · Journal of Industrial Microbiology & Biotechnology · doi:10.1007/bf01575871 · Cited by 385 · see citing works

Ageing of the human metaorganism: the microbial counterpart

Biagi, E., Candela, M., Fairweather‐Tait, S. J., Franceschi, C., & Brigidi, P. (2011) · AGE · doi:10.1007/s11357-011-9217-5 · Cited by 365 · see citing works

Molecular dialogue between the human gut microbiota and the host: a Lactobacillus and Bifidobacterium perspective

Turroni, F., Ventura, M., Buttó, L. F., Duranti, S., O’Toole, P. W., Motherway, M. O., & van Sinderen, D. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-013-1318-0 · Cited by 336 · see citing works

Getting better with bifidobacteria

Leahy, S. C., Higgins, D. G., Fitzgerald, G. F., & van Sinderen, D. (2005) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2005.02600.x · Cited by 331 · see citing works

Taxonomy of Lactobacilli and Bifidobacteria.

Felis, G. E., & Dellaglio, F. (2007) · PubMed · Cited by 326 · see citing works

Manipulating the gut microbiota to maintain health and treat disease

Scott, K. P., Antoine, J., Midtvedt, T., & van Hemert, S. (2015) · Microbial Ecology in Health and Disease · doi:10.3402/mehd.v26.25877 · Cited by 284 · see citing works

Bifidobacteria: their impact on gut microbiota composition and their applications as probiotics in infants

Gioia, D. D., Aloisio, I., Mazzola, G., & Biavati, B. (2013) · Applied Microbiology and Biotechnology · doi:10.1007/s00253-013-5405-9 · Cited by 208 · see citing works

Genomics and ecological overview of the genus Bifidobacterium

Turroni, F., van Sinderen, D., & Ventura, M. (2010) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2010.12.010 · Cited by 197 · see citing works

Recent developments in probiotics: An emphasis on Bifidobacterium

Sharma, M., Wasan, A., & Sharma, R. K. (2021) · Food Bioscience · doi:10.1016/j.fbio.2021.100993 · Cited by 169 · see citing works

Bifidobacterial Dialogue With Its Human Host and Consequent Modulation of the Immune System

Alessandri, G., Ossiprandi, M. C., MacSharry, J. A., van Sinderen, D., & Ventura, M. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2019.02348 · Cited by 128 · see citing works

Gnotobiotic Mouse Immune Response Induced byBifidobacteriumsp. Strains Isolated from Infants

Ménard, O., Butel, M., Gaboriau‐Routhiau, V., & Waligora‐Dupriet, A. (2007) · Applied and Environmental Microbiology · doi:10.1128/aem.01261-07 · Cited by 123 · see citing works

Analysis of 1321 Eubacterium rectale genomes from metagenomes uncovers complex phylogeographic population structure and subspecies functional adaptations

Karcher, N., Pasolli, E., Asnicar, F., Huang, K. D., Tett, A., Manara, S., Armanini, F., Bain, D., Duncan, S. H., Louis, P., et al. (2020) · Genome Biology · doi:10.1186/s13059-020-02042-y · Cited by 116 · see citing works

Bifidobacteria and lactobacilli in human health.

Orrhage, K., & Ce, N. (2000) · PubMed · Cited by 109 · see citing works

Microbial genomes from non-human primate gut metagenomes expand the primate-associated bacterial tree of life with over 1000 novel species

Manara, S., Asnicar, F., Beghini, F., Bazzani, D., Cumbo, F., Zolfo, M., Nigro, E., Karcher, N., Manghi, P., Metzger, M., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1923-9 · Cited by 91 · see citing works

Probiotics in the gastrointestinal diseases of the elderly

Malaguarnera, G., Leggio, F., Vacante, M., Motta, M., Giordano, M., Biondi, A., Basile, F., Mastrojeni, S., Mistretta, A., Malaguarnera, M., et al. (2011) · The journal of nutrition health & aging · doi:10.1007/s12603-011-0357-1 · Cited by 79 · see citing works

Bifidobacterium animalis subsp. lactis 420 for Metabolic Health: Review of the Research

Uusitupa, H., Rasinkangas, P., Lehtinen, M. J., Mäkelä, S. M., Airaksinen, K., Anglenius, H., Ouwehand, A. C., & Maukonen, J. (2020) · Nutrients · doi:10.3390/nu12040892 · Cited by 77 · see citing works

Bifidobacteria-Host Interactions—An Update on Colonisation Factors

Grimm, V., Westermann, C., & Riedel, C. U. (2014) · BioMed Research International · doi:10.1155/2014/960826 · Cited by 54 · see citing works

Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy

Ladeira, R., Tap, J., & Derrien, M. (2023) · Microbiome Research Reports · doi:10.20517/mrr.2023.01 · Cited by 19 · see citing works

Effects of Bifidobacterium animalis subspecies lactis supplementation on gastrointestinal symptoms: systematic review with meta-analysis

Araújo, M. M., Vogado, C. D. O., Mendes, M. M., Gonçalves, V. S. S., & Botelho, P. B. (2021) · Nutrition Reviews · doi:10.1093/nutrit/nuab109 · Cited by 10 · see citing works

Bacteriocin gene-mediated ecological adaptation of Bifidobacterium breve in the adult human gut

Wang, J., Qian, X., Li, Q., Jin, Z., Liu, N., Zhao, J., Chen, W., Wang, S., & Tian, P. (2026) · Cell Genomics · doi:10.1016/j.xgen.2025.101106 · Cited by 5 · see citing works

Genome-scale insights into the metabolic landscape and evolutionary development of Bifidobacterium bifidum

Selleri, E., Longhi, G., Tarracchini, C., Carolis, E. D., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Ventura, M., & Lugli, G. A. (2026) · Microbiome Research Reports · doi:10.20517/mrr.2026.19

FAQ: Human Microbiome

Reid, A. H., & Greene, S. M. (2014) · Cited by 3 · see citing works

Implications of the human microbiome in inflammatory bowel diseases

Bakhtiar, S. M., LeBlanc, J. G., Salvucci, E., Ali, A., Martín, R., Langella, P., Chatel, J., Miyoshi, A., Bermúdez‐Humarán, L. G., & Azevedo, V. (2013) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12111 · Cited by 72 · see citing works

The Human Microbiome Project in 2011 and Beyond

Proctor, L. M. (2011) · Cell Host & Microbe · doi:10.1016/j.chom.2011.10.001 · Cited by 269 · see citing works

Microbiome (Bacterial Community Interactions: Human Microbiota, Human Microbiome, Biofilms)

Sahadulla, M. (2018) · Jaypee Brothers Medical Publishers (P) Ltd. eBooks · doi:10.5005/jp/books/14120_29

The Microbiome—The Explanation for (Almost) Everything?

Shaw, L. P., & Klein, N. J. (2018) · The Pediatric Infectious Disease Journal · doi:10.1097/inf.0000000000002261 · Cited by 3 · see citing works