refs.bib

@article{shaoGenomicAtlasBifidobacterium2026,
  title = {Genomic Atlas of {{Bifidobacterium}} Infantis and {{B}}. Longum Informs Infant Probiotic Design},
  author = {Shao, Yan and Wang, Shuyi and Gichuki, Bonface M. and Stares, Mark D. and Rozday, Timothy J. and Kumar, Nitin and Browne, Hilary P. and Dawson, Nicholas J.R. and Njunge, James M. and Tigoi, Caroline and Ngao, Narshion and Chisti, Mohammod Jobayer and Singa, Benson O. and Kariuki, Samuel and Diallo, Abdoulaye Hama and Saleem, Ali Faisal and Ali, Syed Asad and Mupere, Ezekiel and Mbale, Emmie and Tickell, Kirkby D. and Voskuijl, Wieger P. and Lancioni, Christina L. and Bandsma, Robert H.J. and Ahmed, Tahmeed and Walson, Judd L. and Berkley, James A. and Lawley, Trevor D.},
  year = 2026,
  month = feb,
  journal = {Cell},
  pages = {S0092867426000541},
  issn = {00928674},
  doi = {10.1016/j.cell.2026.01.007},
  urldate = {2026-03-04},
  abstract = {Bifidobacterium longum and B. infantis are pioneer colonizers of the neonatal gut and are widely used as probiotics to support infant growth, development, and disease resistance. However, commercial strains derived largely from high-income countries (HICs) may be suboptimal for infants in low- and middle-income countries (LMICs). We assembled a global genomic atlas of more than 4,000 genomes from 48 countries, increasing representation from LMICs by 12- to 17-fold. High-resolution phylogenomic and functional analyses support delineating B. longum and B. infantis as distinct species with divergent functions and epidemiological patterns. B. infantis dominates early-life microbiota in LMICs but is rarely detected in HICs. Natural B. infantis strains show extreme biogeographic stratification and predicted adaptations to local plant-glycan-rich diets and breast-milk-derived substrates, including urea and B vitamins. This genomic resource enables genomeguided selection of geographically matched strains to inform more effective probiotics and precision microbiome therapeutics for diverse infant populations.},
  langid = {english},
  keywords = {synced},
  file = {/home/kevin/Zotero/storage/5T3NZI54/1-s2.0-S0092867426000541-main.pdf;/home/kevin/Zotero/storage/ETXGUU3U/Shao et al. - 2026 - Genomic atlas of Bifidobacterium infantis and B. longum informs infant probiotic design.pdf}
}

@article{taoEvolutionaryGlycomicsCharacterization2011,
  title = {Evolutionary {{Glycomics}}: {{Characterization}} of {{Milk Oligosaccharides}} in {{Primates}}},
  shorttitle = {Evolutionary {{Glycomics}}},
  author = {Tao, Nannan and Wu, Shuai and Kim, Jaehan and An, Hyun Joo and Hinde, Katie and Power, Michael L. and Gagneux, Pascal and German, J. Bruce and Lebrilla, Carlito B.},
  year = 2011,
  month = apr,
  journal = {Journal of proteome research},
  volume = {10},
  number = {4},
  pages = {1548--1557},
  issn = {1535-3893},
  doi = {10.1021/pr1009367},
  urldate = {2025-09-17},
  abstract = {Free oligosaccharides are abundant components of mammalian milk and have primary roles as prebiotic compounds, in immune defense, and in brain development. Mass spectrometry-based technique is applied to profile milk oligosaccharides from apes (chimpanzee, gorilla, and siamang), new world monkeys (golden lion tamarin and common marmoset), and an old world monkey (rhesus). The purpose of this study was to evaluate the patterns of primate milk oligosaccharide composition from a phylogenetic perspective in order to assess the extent to which the compositions of hMOs derives from ancestral, primate patterns as opposed to more recent evolutionary events. Milk oligosaccharides were quantitated by nanoflow liquid chromatography on chip-based devices. The relative abundances of fucosylated and sialylated milk oligosaccharides in primates were also determined. For a systematic and comprehensive study of evolutionary patterns of milk oligosaccharides, cluster analysis of primate milk was performed using the chromatographic profile. In general, the oligosaccharides in primate milk, including humans, are more complex and exhibit greater diversity compared to the ones in non-primate milk. A detailed comparison of the oligosaccharides across evolution revealed non-sequential developmental pattern, i.e. that primate milk oligosaccharides do not necessarily cluster according to the primate phylogeny. This report represents the first comprehensive and quantitative effort to profile and elucidate the structures of free milk oligosaccharides so that they can be related to glycan function in different primates.},
  pmcid = {PMC3070053},
  pmid = {21214271}
}

@article{tsoTargetedHighresolutionTaxonomic2021,
  title = {Targeted High-Resolution Taxonomic Identification of {{Bifidobacterium}} Longum Subsp. Infantis Using Human Milk Oligosaccharide Metabolizing Genes},
  author = {Tso, Lauren and Bonham, Kevin S and Fishbein, Alyssa and Rowland, Sophie and {Klepac-Ceraj}, Vanja},
  year = 2021,
  journal = {Nutrients},
  volume = {13},
  number = {8},
  pages = {2833},
  publisher = {MDPI},
  file = {/home/kevin/Zotero/storage/9XMUKH6M/Tso et al. - 2021 - Targeted High-Resolution Taxonomic Identification of Bifidobacterium longum subsp. infantis Using Hu.pdf}
}

@article{woodBacterialResponsesOsmotic2015,
  title = {Bacterial Responses to Osmotic Challenges},
  author = {Wood, Janet M.},
  year = 2015,
  month = may,
  journal = {Journal of General Physiology},
  volume = {145},
  number = {5},
  pages = {381--388},
  issn = {1540-7748, 0022-1295},
  doi = {10.1085/jgp.201411296},
  urldate = {2025-09-25},
  langid = {english},
  file = {/home/kevin/Zotero/storage/3F4FW7RZ/Wood - 2015 - Bacterial responses to osmotic challenges.pdf}
}

@incollection{woodOsmoticStress2014,
  title = {Osmotic {{Stress}}},
  booktitle = {Bacterial {{Stress Responses}}},
  author = {Wood, Janet M.},
  editor = {Storz, Gisela and Hengge, Regine},
  year = 2014,
  month = apr,
  pages = {133--156},
  publisher = {ASM Press},
  address = {Washington, DC, USA},
  doi = {10.1128/9781555816841.ch9},
  urldate = {2025-09-25},
  isbn = {978-1-68367-121-3 978-1-55581-684-1 978-1-55581-621-6},
  langid = {english},
  file = {/home/kevin/Zotero/storage/ZF44SZZG/Wood - 2014 - Osmotic Stress.pdf}
}