Genome-scale analyses of health-promoting bacteria: probiogenomics

Ventura, Marco, O'Flaherty, Sarah, Claesson, Marcus J., Turroni, Francesca, Klaenhammer, Todd R., van Sinderen, Douwe, O'Toole, Paul W.·2009·Nature Reviews Microbiology
DOI 10.1038/nrmicro2047

Cited by (480)

Items 401–480 of 480

  1. Lactobacillus salivarius MZ27 enhances the host's resistance to DSS by modulating the gut microbiota and the AHR/GPX4 signaling pathway
    Yusong Zheng, Xinlin Wang, Runze Liu, Mengqi Zhang, Xingrui Qu, Guodong Sun, Teng Teng, Baoming Shi · 2025 · Food & Function
  2. A Review of Gut Microbiota Dynamics: From Healthy Gestation to Gestational Diabetes in Human and Mouse Models
    Dat Da Ly, Bryony A. McNeill, Kathryn Aston‐Mourney, Leni R. Rivera · 2026 · Biomedicines
  3. Probiogenomic and pangenome characterization of Latilactobacillus sakei subsp. sakei from cabbage kimchi: Insights into probiotic potential and safety attributes
    Priyanka Sharma, Anshul Sharma, Hae‐Jeung Lee · 2026 · Food Bioscience
  4. Chapter 18 Cross-feeding during human colon fermentation
    Luc De Vuyst, Frédéric Leroy · 2019 · Wageningen Academic Publishers eBooks
  5. High-throughput technologies in probiotics science
    Paolo Stincone, Adriano Brandelli, Maria De Angelis · 2022 · Elsevier eBooks
  6. Nanoplastics, Gut Microbiota, and Neurodegeneration
    Ananya Rai · 2022 · Nutritional neurosciences
  7. MCHAN: Prediction of Human Microbe-drug Associations Based on Multiview Contrastive Hypergraph Attention Network
    Guanghui Li, Ziyan Cao, Cheng Liang, Qiu Xiao, Jiawei Luo · 2024 · Current Bioinformatics
  8. GeO2/SiO2 matrix biosensor for detection of probiotic bacteria L. plantarum
    B. Gopal Krishna, Mokka Jagannadha Rao, B. Nalinikant, Devendra Kumar Golhani, S.A.H. Zaidi · 2016 · IEEE Region 10 Conference (TENCON)
  9. Probiotics: The Effects on Human Health and Current Prospects
    Giselle Nobre, Lúcia Helena da Silva Miglioranza · 2012 · InTech eBooks
  10. Analysis of infant isolates of Bifidobacterium breve by comparative genome hybridization indicates the existence of new subspecies with marked infant specificity
    Rolf J. Boesten, Frank H. J. Schuren, Richèle D. Wind, Jan Knol, Willem M. de Vos · 2011 · Research in Microbiology
  11. Genetic Engineering of Probiotic Microorganisms
    Thushara Chathuranga Bamunuarachchige, H.A.M. Wickramasinghe, D. M. J. C. Dissanayaka, N. A. D. Wickramarathna · 2011 · Microbiology monographs
  12. Comparative genomics study of Lactobacillus plantarum strains provides perspectives about proteins involved in the probiogenomics
    Carlos Leonardo Araújo, Samuel Cavalcante do Amaral, Tayná Novaes, Géssica Faial, Larissa Maranhão Dias, Ingrid Coutinho · 2020 · Brazilian Journal of Development
  13. Functional metagenomic analysis of carbohydrate degrading enzymes from the human gut microbiota
    Anna Szczepańska · 2011 · UEA Digital Repository (University of East Anglia)
  14. Women's health is a team effort: probiogenomics supports the development of a multi-species vaginal probiotic
    Calvanese, Chiara Maria, Valentino, Vincenzo, De Prisco, Annachiara, Allesina, Serena, Amoruso, Angela, Deidda, Francesca, Visciglia, Annalisa, Ercolini, Danilo, Pane, Marco, De Filippis, Francesca · 2026 · Cellular and Molecular Life Sciences
  15. AAHLDMA: Predicting Drug-Microbe Associations Based on Bridge Graph Learning
    Yaojia Chen, Mengting Niu, Yi Liu, Jiacheng Wang, Yijie Ding, Quan Zou · 2024 · Lecture notes in computer science
  16. Changes in blood physiological and biochemical parameters and intestinal flora in newborn horses and mares with angular limb deformities
    Yuhui Ma, Yigang Liu, Li Hai, Yang Kailun, Gang Yao · 2024 · Frontiers in Veterinary Science
  17. Multicenter exploration of microbial communities in hospital toilets reveals: antibiotic exposure in nosocomial settings selects for Enterococcus over commensal taxa
    Claudio Neidhöfer, Marcel Neuenhoff, Esther Sib, Anna Rehm, Lúcia Ribeiro Dias, Bernd Neumann, Jörg Steinmann, Manuel Döhla, Yousra Kherabi, Ana Budimir et al. · 2025 · Antimicrobial Resistance and Infection Control
  18. GAALSMDA: A Graph Attention-based Fusion Network Integrating Dual Attention and BiLSTM for Microbe-Drug Association Prediction
    Chunling Xiang, Gaoning Shen, Lei Wang, Xianyou Zhu · 2025 · Current Bioinformatics
  19. Metabolic pathway analysis reveals hierarchical pentose sugar utilization and metabolic flexibility of Bifidobacterium longum
    Lisa Friess, Fionnuala Mary McAuliffe, Paul D. Cotter, Anthony L. Shiver, Kerwyn Casey Huang, Anne de Jong, Douwe van Sinderen · 2026 · Gut Microbes
  20. Selective Breeding of Oxygen-Tolerant and Oxalate-Degrading Lactic Acid Bacteria by Protoplast Fusion
    Sheng Chen, Yu Li, Wenbin Jin, Yan Chen, Xiao Guang Liu, Fu Ping Lu · 2013 · Advanced materials research
  21. Pulsed Field Gel Electrophoresis for Bifidobacterium
    Esther Jiménez, Marta Gómez, Laura Moles · 2015 · Methods in molecular biology
  22. The Double Face of Bacteria and the Ambiguous Role of Some Probiotics
    2014 · CRC Press eBooks
  23. Fermented Dairy Products
    2007
  24. Prediction of Human Microbe-Drug Association based on Layer Attention Graph Convolutional Network
    Jia Qu, Jie Ni, Tongguang Ni, Zekang Bian, Jiuzhen Liang · 2023 · Current Medicinal Chemistry
  25. Probiotic Lactobacillus acidophilus NCFM and Bifidobacterium animalis subsp lactis Bl-04 interactions with prebiotic carbohydrates using differential proteomics and protein characterization
    Morten Ejby · 2012
  26. Efeito de uma bebida probiótica (Enterococcus faecium CRL 183 e Bifidobacterium longum ATCC 15707) à base de extrato aquoso de soja no desenvolvimento de colite quimicamente induzida em ratos
    Larissa Sbaglia Celiberto · 2014 · Americanae (AECID Library)
  27. Lactic Acid Bacteria and the Human Intestinal Microbiome
    François P. Douillard, Willem M. de Vos · 2015
  28. Avaliação da participação dos mircro-organismos da classe Mollicutes na microbiota intestinal de mulheres eutróficas e obesas.
    Verena Macedo Santos · 2016
  29. Frühgeburt und Infektionen
    Ljubomir Petričević · 2014 · Der Gynäkologe
  30. Dietary effects on human fecal microbiota
    Catarina Simões · 2013 · Työväentutkimus Vuosikirja
  31. Computational genomics of lactobacilli
    Matti Kankainen · 2015 · Työväentutkimus Vuosikirja
  32. MOLECULAR BIOLOGY | Genomics
    B.A. Neville, Paul William O’Toole · 2014 · Encyclopedia of Food Microbiology
  33. Lactobacillus crispatus and Propionibacterium freudenreichii: A Genomic and Transcriptomic View
    Teija Ojala · 2016 · Työväentutkimus Vuosikirja
  34. Intestinal nutrient transport in the cradle of the Mediterranean Diet: 23rd EITG meeting report
    2010 · Genes & Nutrition
  35. Metabolomics as a tool to explore the staphylococcal biofilm
    Laurence H. Stipetic · 2016 · Enlighten: Theses (The University of Glasgow)
  36. Development of Bifidobacterium spp. in infants: Age dependent patterns and correlating factors
    Ekaterina Avershina · 2011 · NORA - Norwegian Open Research Archives
  37. The role of the pangenome concept in selecting new starter cultures
    Antonio Bevilacqua, Francesca Fuccio, Maria Clara Iorio, Martina Loi, Milena Sinigaglia · 2017
  38. The Impact of Bifidobacterium bifidum and its Surface Protein BopA on the Murine Intestinal Barrier and Endogenous Microbiota Composition
    Christopher Villa · 2012 · TSpace (University of Toronto)
  39. Metabolic modeling to understand and redesign microbial systems
    Ruben G. A. van Heck · 2017
  40. Estudio y comparación de la microbiota intestinal en individuos no celiacos frente a pacientes diagnosticados de enfermedad celiaca = Study and comparison of the intestinal microbiota in non celiac individuals and patients with celiac disease
    Esther Nistal · 2011
  41. Comparative Genomic Analyses of Lactic Acid Bacteria
    Wei Chen, Hongchao Wang · 2019 · Springer eBooks
  42. Comprehensive analysis of microbes and metabolites in human tear fluids
    慎之介 村上, 藤貴 馬場, Wanping Aw, 真嗣 福田, 朋義 曽我, 浩 藤島, 勝 冨田 · 2015 · Institutional Repositories DataBase (IRDB)
  43. Beneficial microbes from human and animal intestines
    Sofía Fernández-Ciganda, Martín Fraga, Pablo Zunino · 2022 · Elsevier eBooks
  44. Peer Review #2 of "Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi) (v0.1)"
    2021 · PeerJ
  45. Peer Review #1 of "Diverse methanogens, bacteria and tannase genes in the feces of the endangered volcano rabbit (Romerolagus diazi) (v0.1)"
    2021 · PeerJ
  46. Peer Review #1 of "Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction (v0.2)"
    2022 · PeerJ
  47. Peer Review #2 of "Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction (v0.1)"
    2022 · PeerJ
  48. Peer Review #1 of "Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction (v0.1)"
    2022 · PeerJ
  49. Peer Review #2 of "Neighborhood-based inference and restricted Boltzmann machine for microbe and drug associations prediction (v0.2)"
    2022 · PeerJ
  50. Genomic Analysis of Lactiplantibacillus Pentosus LTJ12, a Novel Strain with High Alcohol Tolerance Isolated from Chinese Baijiu
    Jiali Wang, Chengshun Lu, Qiang Xu, Zhong-Yuan Li, Yajian Song, Sa Zhou, Zhao Shuxian, Jiqi Li, Xuegang Luo, Tong‐Cun Zhang · 2022 · SSRN Electronic Journal
  51. ASSESSMENT OF VACCINATION IMPACT ON HEPATITIS B EPIDEMIOLOGY IN THE REPUBLIC OF BELARUS
    Veronika S Vysotskaya, Natalia D Kolomiets, Irina N. Glinskaya, O. N. Romanova, Гасич Елена Леонидовна, Elena Samoilovich · 2023 · Hepatology and Gastroenterology
  52. EFFECT OF MEROPENEM AND IMICENEM ON MICROBIOCENOSIS AND MORPHOLOGY OF THE SMALL INTESTINE IN RATS
    V. M. Sheibak, A. V. Lemesh, I. V. Nikolaeva, R. E. Yakubtsevich, O. B. Ostrovskaya · 2023 · Hepatology and Gastroenterology
  53. Characterization of bacillus isolates using whole genome sequencing analysis and application as a potential food probiotic
    Gauri Khullar · 2019
  54. Metabolic Engineering of Bifidobacterium sp. Using Genome Editing Techniques
    Aravind Sundararaman, Prakash Motiram Halami · 2024 · BENTHAM SCIENCE PUBLISHERS eBooks
  55. Additional file 1 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  56. Additional file 6 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  57. Additional file 3 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  58. Additional file 8 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Wang, Lei · 2023 · Figshare
  59. Additional file 3 of Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model
    Yue Xiao, Chao Yang, Leilei Yu, Fengwei Tian, Yarong Wu, Jianxin Zhao, Hao Zhang, Ruifu Yang, Wei Chen, Colin Hill et al. · 2021 · Figshare
  60. Additional file 4 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  61. Additional file 7 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  62. Additional file 5 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Wang, Lei · 2023 · Figshare
  63. Additional file 2 of GACNNMDA: a computational model for predicting potential human microbe-drug associations based on graph attention network and CNN-based classifier
    Qing Ma, Yaqin Tan, Lei Wang · 2023 · Figshare
  64. Microbe-Drug Association Prediction Model Based on Graph Convolutional Network and Graph Attention Network
    Bo Wang, Tongxuan Wang, Xiaoxin Du, Jingwei Li, Junqi Wang, Peilong Wu · 2024 · SSRN Electronic Journal
  65. GVNNVAE: A Novel Microbe-Drug Association Prediction Model based on an Improved Graph Neural Network and the Variational Auto-Encoder
    Yi‐Ming Chen, Zhen Zhang, Xin Liu, Bin Zeng, Lei Wang · 2024 · Current Bioinformatics
  66. Future prospective of microbiome-gut brain axis for treatment of CNS disorders
    Ramdas Mane, Saurabh Kashid, Farhan Mazahir, Awesh Kumar Yadav · 2025 · Elsevier eBooks
  67. The comprehensive role of probiotic-derived peptides in immunomodulation
    Burcu Tekin, Rafig Gurbanov, Ozdemir, Fadime · 2025 · Studies in natural products chemistry
  68. HAFMMDA: HIN2vec-Based Attentional Factorization Machines for Predicting Microbe-Drug Associations
    Bo Wang, Junqi Wang, Xiaoxin Du, Jianfei Zhang, Yang He, Fangjian Ma · 2025 · Interdisciplinary Sciences Computational Life Sciences
  69. Probiotics
    Denis Roy, Joseph Lupien‐Meilleur · 2025 · Elsevier eBooks
  70. Structural and functional characterisation of mucus adhesion proteins of Lactobacillus reuteri
    Sabrina Etzold · 2013 · UEA Digital Repository (University of East Anglia)
  71. Additional file 1 of The metabolic profile of Bifidobacterium dentium reflects its status as a human gut commensal
    Melinda Anne Engevik, Danhof, Heather A., Anne E. Hall, Kristen A. Engevik, Thomas D. Horvath, Haidacher, Sigmund J., Kathleen M. Hoch, Bradley T. Endres, Bajaj, Meghna, Kevin W. Garey et al. · 2021 · Figshare
  72. Additional file 2 of Human gut-derived B. longum subsp. longum strains protect against aging in a d-galactose-induced aging mouse model
    Xiao, Yue, Yang, Chao, Yu, Leilei, Tian, Fengwei, Wu, Yarong, Zhao, Jianxin, Hao Zhang, Ruifu Yang, Wei Chen, Colin Hill et al. · 2021 · Figshare
  73. Hypergraph contrastive learning with optimal transport: an effective hypergraph contrastive learning framework for deciphering complicated microbe-drug interaction relationships
    Yuanyuan Ma, Lifang Liu · 2026 · PeerJ Computer Science
  74. Gut-brain axis in metabolic control
    S. P. Singh, Shampa Ghosh, Dr. Krishna Kumar Singh, Jitendra Kumar Sinha · 2026 · Elsevier eBooks
  75. Unveiling the Probiotic Properties of Lacticaseibacillus paracasei UFTM 2.9 Through Probiogenomic Analysis
    Bárbara Ribeiro Fonseca, Yasmin Neves Vieira Sabino, Beatriz M. O. Rocha, Vasco A. C. Azevedo, Bertram Brenig, Siomar de Castro Soares, Leandro Nascimento Lemos, Lívia Bordalo Tonucci, Sheila Cristina Potente Dutra Luquetti, Aline Dias Paiva et al. · 2026 · Molecular Nutrition & Food Research
  76. Immuno-Modulation Properties of Lactobacillus delbrueckii
    Clarissa Santos Rocha · 2011 · theses.fr (ABES)
  77. Probiotiques, prébiotiques, synbiotiques et prévention des maladies inflammatoires chroniques de l'intestin : proposition d'un crible de sélection rationnel in vitro
    Julien Grimoud · 2010
  78. Potentiel probiotique des bactéries lactiques de l'écosystème mammaire bovin contre les mammites à Staphylococcus aureus
    Damien S. Bouchard · 2013 · theses.fr (ABES)
  79. Comparative Genomics of Faecalibacterium spp.
    Leandro Benevides · 2018
  80. Proteomic and Metabolomic Perspectives on Microbial Function
    Ranbir Chander Sobti, Mohammed Azhar Khan · 2026 · Springer eBooks