
Catanzaro, J. R. et al. IgA-deficient humans exhibit gut microbiota dysbiosis despite secretion of compensatory IgM. Sci. Rep. 9, 13574 (2019).
Macpherson, A. J., McCoy, K. D., Johansen, F.-E. & Brandtzaeg, P. The immune geography of IgA induction and function. Mucosal Immunol. 1, 11–22 (2008).
Sender, R. et al. The total mass, number, and distribution of immune cells in the human body. Proc. Natl Acad. Sci. USA 120, e2308511120 (2023).
Conrey, P. E. et al. IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation. Sci. Immunol. 8, eade2335 (2023).
Fadlallah, J. et al. Microbial ecology perturbation in human IgA deficiency. Sci. Transl. Med. 10, eaan1217 (2018).
Yel, L. Selective IgA deficiency. J. Clin. Immunol. 30, 10–16 (2010).
Palm, N. W. et al. Immunoglobulin A coating identifies colitogenic bacteria in inflammatory bowel disease. Cell 158, 1000–1010 (2014).
Huus, K. E. et al. Immunoglobulin recognition of fecal bacteria in stunted and non-stunted children: findings from the Afribiota study. Microbiome 8, 113 (2020).
Shapiro, J. M. et al. Immunoglobulin A targets a unique subset of the microbiota in inflammatory bowel disease. Cell Host Microbe 29, 83–93.e3 (2021).
Yang, C. et al. Immunoglobulin A antibody composition is sculpted to bind the self gut microbiome. Sci. Immunol. 7, eabg3208 (2022).
Weis, A. M. & Round, J. L. Microbiota–antibody interactions that regulate gut homeostasis. Cell Host Microbe 29, 334–346 (2021).
Moor, K. et al. High-avidity IgA protects the intestine by enchaining growing bacteria. Nature 544, 498–502 (2017).
Macpherson, A. J. & Uhr, T. Induction of protective IgA by intestinal dendritic cells carrying commensal bacteria. Science 303, 1662–1665 (2004).
Rollenske, T. et al. Parallelism of intestinal secretory IgA shapes functional microbial fitness. Nature 598, 657–661 (2021).
Huus, K. E. et al. Commensal bacteria modulate immunoglobulin A binding in response to host nutrition. Cell Host Microbe 27, 909–921.e5 (2020).
Joglekar, P. et al. Intestinal IgA regulates expression of a fructan polysaccharide utilization locus in colonizing gut commensal Bacteroides thetaiotaomicron. MBio 10, e02324-19 (2019).
Donaldson, G. P. et al. Gut microbiota utilize immunoglobulin A for mucosal colonization. Science 360, 795–800 (2018).
McLoughlin, K., Schluter, J., Rakoff-Nahoum, S., Smith, A. L. & Foster, K. R. Host selection of microbiota via differential adhesion. Cell Host Microbe 19, 550–559 (2016).
Bansept, F. et al. Enchained growth and cluster dislocation: a possible mechanism for microbiota homeostasis. PLoS Comput. Biol. 15, e1006986 (2019).
Bunker, J. J. & Bendelac, A. IgA responses to microbiota. Immunity 49, 211–224 (2018).
Gopalakrishna, K. P. et al. Maternal IgA protects against the development of necrotizing enterocolitis in preterm infants. Nat. Med. 25, 1110–1115 (2019).
Korem, T. et al. Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples. Science 349, 1101–1106 (2015).
Brown, C. T., Olm, M. R., Thomas, B. C. & Banfield, J. F. Measurement of bacterial replication rates in microbial communities. Nat. Biotechnol. 34, 1256–1263 (2016).
Jackson, M. A. et al. Accurate identification and quantification of commensal microbiota bound by host immunoglobulins. Microbiome 9, 33 (2021).
Bunker, J. J. et al. B cell superantigens in the human intestinal microbiota. Sci. Transl. Med. 11, eaau9356 (2019).
Wastyk, H. C. et al. Gut-microbiota-targeted diets modulate human immune status. Cell 184, 4137–4153.e14 (2021).
Bunker, J. J. et al. Natural polyreactive IgA antibodies coat the intestinal microbiota. Science 358, eaan6619 (2017).
Planer, J. D. et al. Development of the gut microbiota and mucosal IgA responses in twins and gnotobiotic mice. Nature 534, 263–266 (2016).
Wilmore, J. R. et al. Commensal microbes induce serum IgA responses that protect against polymicrobial sepsis. Cell Host Microbe 23, 302–311.e3 (2018).
Almeida, D. et al. Evolving trends in next-generation probiotics: a 5W1H perspective. Crit. Rev. Food Sci. Nutr. 60, 1783–1796 (2020).
Henrick, B. M. et al. Bifidobacteria-mediated immune system imprinting early in life. Cell 184, 3884–3898.e11 (2021).
Yu, L. et al. Molecular cloning and functional characterization of an ATP-binding cassette transporter OtrC from Streptomyces rimosus. BMC Biotechnol. 12, 52 (2012).
Declerck, N., Vincent, F., Hoh, F., Aymerich, S. & van Tilbeurgh, H. RNA recognition by transcriptional antiterminators of the BglG/SacY family: functional and structural comparison of the CAT domain from SacY and LicT. J. Mol. Biol. 294, 389–402 (1999).
Tailford, L. E., Crost, E. H., Kavanaugh, D. & Juge, N. Mucin glycan foraging in the human gut microbiome. Front. Genet. 6, 81 (2015).
Saez-Lara, M. J., Gomez-Llorente, C., Plaza-Diaz, J. & Gil, A. The role of probiotic lactic acid bacteria and bifidobacteria in the prevention and treatment of inflammatory bowel disease and other related diseases: a systematic review of randomized human clinical trials. BioMed. Res. Int. 2015, 505878 (2015).
Takeuchi, T. et al. Acetate differentially regulates IgA reactivity to commensal bacteria. Nature 595, 560–564 (2021).
Morita, N. et al. GPR31-dependent dendrite protrusion of intestinal CX3CR1+ cells by bacterial metabolites. Nature 566, 110–114 (2019).
Kubinak, J. L. et al. MyD88 signaling in T cells directs IgA-mediated control of the microbiota to promote health. Cell Host Microbe 17, 153–163 (2015).
Nakajima, A. et al. IgA regulates the composition and metabolic function of gut microbiota by promoting symbiosis between bacteria. J. Exp. Med. 215, 2019–2034 (2018).
Huang, J. Y., Lee, S. M. & Mazmanian, S. K. The human commensal Bacteroides fragilis binds intestinal mucin. Anaerobe 17, 137–141 (2011).
An, D. et al. Sphingolipids from a symbiotic microbe regulate homeostasis of host intestinal natural killer T cells. Cell 156, 123–133 (2014).
Bae, M. et al. Akkermansia muciniphila phospholipid induces homeostatic immune responses. Nature 608, 168–173 (2022).
Singh, V. et al. Butyrate producers, ‘The Sentinel of Gut’: their intestinal significance with and beyond butyrate, and prospective use as microbial therapeutics. Front. Microbiol. 13, 1103836 (2022).
Chen, S., Zhou, Y., Chen, Y. & Gu, J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics 34, i884–i890 (2018).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Luk, A. W., Beckmann, S. & Manefield, M. Dependency of DNA extraction efficiency on cell concentration confounds molecular quantification of microorganisms in groundwater. FEMS Microbiol. Ecol. 94, fiy146 (2018).
Nurk, S., Meleshko, D., Korobeynikov, A. & Pevzner, P. A. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 27, 824–834 (2017).
Gurevich, A., Saveliev, V., Vyahhi, N. & Tesler, G. QUAST: quality assessment tool for genome assemblies. Bioinformatics 29, 1072–1075 (2013).
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Olm, M. R., Brown, C. T., Brooks, B. & Banfield, J. F. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 11, 2864–2868 (2017).
Almeida, A. et al. A unified catalog of 204,938 reference genomes from the human gut microbiome. Nat. Biotechnol. 39, 105–114 (2020).
Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P. & Parks, D. H. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics https://doi.org/10.1093/bioinformatics/btz848 (2019).
Olm, M. R. et al. inStrain profiles population microdiversity from metagenomic data and sensitively detects shared microbial strains. Nat. Biotechnol. https://doi.org/10.1038/s41587-020-00797-0 (2021).
Hunter, J. D. Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90–95 (2007).
Ondov, B. D. et al. Mash: fast genome and metagenome distance estimation using MinHash. Genome Biol. 17, 132 (2016).
Jones, E., Oliphant, T. & Peterson, P. SciPy: open source scientific tools for Python. http://scipy.org (2001).
Lee, M. D. GToTree: a user-friendly workflow for phylogenomics. Bioinformatics 35, 4162–4164 (2019).
Moshiri, N. TreeSwift: a massively scalable Python tree package. SoftwareX 11, 100436 (2020).
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 23, 127–128 (2007).
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. https://doi.org/10.1093/nar/gky995 (2018).
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2020).
Jia, B. et al. CARD 2017: expansion and model-centric curation of the comprehensive antibiotic resistance database. Nucleic Acids Res. 45, D566–D573 (2017).
Drula, E. et al. The carbohydrate-active enzyme database: functions and literature. Nucleic Acids Res. 50, D571–D577 (2022).
Gellman, R. H. et al. Hadza Prevotella require diet-derived microbiota-accessible carbohydrates to persist in mice. Cell Rep. 42, 113233 (2023).
Olm, M. Data supporting publication ‘Metagenomic immunoglobulin sequencing (MIG-Seq) exposes patterns of IgA antibody binding in the healthy human gut microbiome’. Zenodo https://doi.org/10.5281/ZENODO.11154974 (2023).
Olm, M. MrOlm/MIGSeq_code: Version 1.1 (1.1). Zenodo https://doi.org/10.5281/zenodo.14269815 (2024).
- SEO Powered Content & PR Distribution. Get Amplified Today.
- PlatoData.Network Vertical Generative Ai. Empower Yourself. Access Here.
- PlatoAiStream. Web3 Intelligence. Knowledge Amplified. Access Here.
- PlatoESG. Carbon, CleanTech, Energy, Environment, Solar, Waste Management. Access Here.
- PlatoHealth. Biotech and Clinical Trials Intelligence. Access Here.
- Source: https://www.nature.com/articles/s41564-024-01887-4