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Bacteroides fragilis (B. fragilis) is an obligate anaerobic bacterium that is part of the normal human gut microbiome. It is a well-characterized strain commonly used in research and clinical applications.

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Lab products found in correlation

P aeruginosa, by American Type Culture Collection (3 mentions) S agalactiae, by American Type Culture Collection (3 mentions) S aureus, by American Type Culture Collection (3 mentions) E faecalis, by American Type Culture Collection (3 mentions) Anti flag antibody, by Merck Group (2 mentions) S pyogenes, by American Type Culture Collection (2 mentions) E coli, by American Type Culture Collection (2 mentions) V cholerae, by American Type Culture Collection (2 mentions) K pneumoniae, by American Type Culture Collection (2 mentions) A baumannii, by American Type Culture Collection (2 mentions) S pneumoniae, by American Type Culture Collection (2 mentions) B subtilis, by American Type Culture Collection (2 mentions) C difficile, by American Type Culture Collection (2 mentions) L rhamnosus, by American Type Culture Collection (1 mentions) S saprophyticus, by American Type Culture Collection (1 mentions) Ags cells, by American Type Culture Collection (1 mentions)

6 protocols using b fragilis

1

Synthesis of Glycan Chemical Probes

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Organic chemicals and anti-FLAG antibodies were purchased from Sigma-Aldrich. H. pylori strain G2751 (link) was a gift of Manuel Amieva (Stanford University), and M. smegmatis strain Mc2155::otsA treS treY52 (link) was a gift from Peter Woodruff (University of Southern Maine). Bacterial cells (C. jejuni ATCC 33560; B. thailandensis ATCC 700388; R. solanacearum ATCC 33291* (*incorrectly cataloged as C. jejuni; species confirmed as R. solanacearum by 16S ribosomal RNA sequencing); B. fragilis ATCC 23745; P. aeruginosa ATCC 39324) and MDCK cells (ATCC CCL-34) were purchased from ATCC and grown according to the supplier’s instructions. Ac4GlcNAc (1), Ac4GlcNAz (2), Ac4GalNAz and Phos-FLAG were synthesized as previously described.19 ,53 Ac36AzGlcNAc (3)42 (link) was kindly provided by Matthew Pratt (University of Southern California). Ac3FucNAz (4), Ac2Bac-diNAz (5), and Ac2DATDG-diNAz (6) were synthesized using standard organic chemistry procedures and characterized by standard techniques including 1H and 13C NMR spectroscopy and mass spectrometry. Ac3FucNAz (4), Ac2Bac-diNAz (5), and Ac2DATDG-diNAz (6) were purified using flash silica gel chromatography.
Clark E.L., Emmadi M., Krupp K.L., Podilapu A.R., Helble J.D., Kulkarni S.S, & Dube D.H. (2016). Development of rare bacterial monosaccharide analogs for metabolic glycan labeling in pathogenic bacteria. ACS chemical biology, 11(12), 3365-3373.
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2

Culturing Diverse Anaerobic and Aerobic Bacteria

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Akk (DSM 22959) and B. thetaiotaomicron (VPI-5482) were cultured in brain heart infusion (BHI) broth. B. vulgatus [American Type Culture Collection (ATCC) 8482] was cultured in BHI broth supplemented with cysteine-HCl (1 mg/ml), hemin (0.015 mg/ml), and yeast extract (BHI+) (5 mg/ml). B. acidifaciens (JCM 10556) was cultured in Gifu anaerobic medium (GAM). B. fragilis (ATCC 25285) was cultured in modified GAM. E. coli (Nissle 1917) and S. typhimurium (SL1344) were cultured in LB broth. Akk, B. thetaiotaomicron, B. vulgatus, B. acidifaciens, and B. fragilis were cultured under anaerobic conditions at 37°C, while E. coli and S. typhimurium were under normoxic environments. Caco-2 and HT-29-MTX-E12 cells were cultured with Dulbecco’s modified Eagle’s medium (DMEM) containing 10% fetal bovine serum (FBS), streptomycin (100 mg/ml), penicillin (100 U/ml), and 1% nonessential amino acid. CT-26 cells were cultured with DMEM containing 10% FBS, streptomycin (100 mg/ml), and penicillin (100 U/ml).
Wang X., Lin S., Wang L., Cao Z., Zhang M., Zhang Y., Liu R, & Liu J. (2023). Versatility of bacterial outer membrane vesicles in regulating intestinal homeostasis. Science Advances, 9(11), eade5079.
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3

Gut Microbiome Colonization in Mice

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The bacteria taxa termed “Lachnospiraceae” in this study were a mixture of 23 strains that belong to the family Lachnospiraceae as previously reported (11 (link)) unless otherwise noted. These bacteria were cultured in an anaerobic chamber in BHI broth supplemented with 5% fetal bovine serum, 0.01% L-cysteine, and 1% corn starch. E. faecalis (ATCC #19433), L. rhamnosus (ATCC #53103), B. fragilis (ATCC #23745), S. aureus (ATCC #25904), S. saprophyticus (ATCC #49907), and S. agalactiae (ATCC #13813) were purchased from ATCC and cultured according to the manufacturer’s instructions. SPF C57BL/6J mice first received antibiotic treatment (20 mg of streptomycin per mouse) by oral gavage. One day later, mice were gavaged with the indicated strains twice a week for 8 weeks. BHI medium was used as a vehicle control. After the last administration, recipients were treated with a high dose of total body radiation.
Guo H., Chou W.C., Lai Y., Liang K., Tam J.W., Brickey W.J., Chen L., Montgomery N.D., Li X., Bohannon L.M., Sung A.D., Chao N.J., Peled J.U., Gomes A.L., van den Brink M.R., French M.J., Macintyre A.N., Sempowski G.D., Tan X., Sartor R.B., Lu K, & Ting J.P. (2020). Multi-omics analyses of radiation survivors identify radioprotective microbes and metabolites. Science (New York, N.Y.), 370(6516), eaay9097.
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4

Bacterial Glycan Biosynthesis Protocols

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Organic chemicals
and anti-FLAG antibodies were purchased from Sigma-Aldrich. H. pylori strain G2758 (link) was a gift of Manuel Amieva (Stanford University). B. fragilis (ATCC 23745) and AGS cells (ATCC CRL-1739)
were purchased from ATCC and grown according to the supplier’s
instructions. Ac4GlcNAc, Ac4GlcNAz, Ac4GalNAz, and Phos-FLAG were synthesized as previously described.17 (link),59 (link),60 (link) BacSBn 4, DATSBn 5, and FucSBn
6 were synthesized by using standard organic chemistry procedures
and characterized by standard techniques including 1H and 13C NMR spectroscopy and mass spectrometry. Analogues 4–6
were purified using flash silica gel chromatography.
Quintana I.D., Paul A., Chowdhury A., Moulton K.D., Kulkarni S.S, & Dube D.H. (2023). Thioglycosides Act as Metabolic Inhibitors of Bacterial Glycan Biosynthesis. ACS Infectious Diseases, 9(10), 2025-2035.
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5

Antibacterial and Antiviral Efficacy Determination

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Antibacterial assays were carried out by Micromyx, LLC in accordance with methods from the Clinical and Laboratory Standards Institute. Minimal inhibitory concentrations were determined with the following strains (listed in Table 1 and Supplementary Table 14): S. aureus ATCC 29213, S. aureus MMX 2011, S. pneumoniae ATCC 49619, S. pyogenes MMX 6253, S. agalactiae MMX 6189, E. faecalis ATCC 29212, E. faecalis MMX 486, B. subtilis ATCC 6633, E. coli ATCC 25922, K. pneumoniae MMX 214, P. aeruginosa ATCC 27853, A. baumannii ATCC 19606, V. cholerae BAA-2163, C. difficile ATCC 700057, and B. fragilis ATCC 25285.
Antiviral assays were performed by Virapur in accordance with methods from the Clinical and Laboratory Standards Institute. Minimal inhibitory concentrations were determined with the following viruses and host cells (listed in Table 1 and Supplementary Table 14): Influenza A/Perth/16/2009 in MDCK cells, Influenza B/Wisconsin/1/2010 in MDCK cells, Herpes Simplex 1 Strain MacIntyre in Vero cells, Herpex Simplex 2 Strain G in Vero cells, Vaccinia virus WR in Vero cells, Rhinovirus 8 in HeLa cells and Respiratory Syncytial Virus in Hep2 cells.
All assays (antibacterial and antiviral) were carried out in triplicates and yielded identical MIC values for all replicates (Table 1). As such a range or an error was not available to report.
Xu F., Wu Y., Zhang C., Davis K.M., Moon K., Bushin L.B, & Seyedsayamdost M.R. (2019). A Genetics-Free Method for High-Throughput Discovery of Cryptic Microbial Metabolites. Nature chemical biology, 15(2), 161-168.
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6

Antibacterial and Antiviral Efficacy Determination

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Antibacterial assays were carried out by Micromyx, LLC in accordance with methods from the Clinical and Laboratory Standards Institute. Minimal inhibitory concentrations were determined with the following strains (listed in Table 1 and Supplementary Table 14): S. aureus ATCC 29213, S. aureus MMX 2011, S. pneumoniae ATCC 49619, S. pyogenes MMX 6253, S. agalactiae MMX 6189, E. faecalis ATCC 29212, E. faecalis MMX 486, B. subtilis ATCC 6633, E. coli ATCC 25922, K. pneumoniae MMX 214, P. aeruginosa ATCC 27853, A. baumannii ATCC 19606, V. cholerae BAA-2163, C. difficile ATCC 700057, and B. fragilis ATCC 25285.
Antiviral assays were performed by Virapur in accordance with methods from the Clinical and Laboratory Standards Institute. Minimal inhibitory concentrations were determined with the following viruses and host cells (listed in Table 1 and Supplementary Table 14): Influenza A/Perth/16/2009 in MDCK cells, Influenza B/Wisconsin/1/2010 in MDCK cells, Herpes Simplex 1 Strain MacIntyre in Vero cells, Herpex Simplex 2 Strain G in Vero cells, Vaccinia virus WR in Vero cells, Rhinovirus 8 in HeLa cells and Respiratory Syncytial Virus in Hep2 cells.
All assays (antibacterial and antiviral) were carried out in triplicates and yielded identical MIC values for all replicates (Table 1). As such a range or an error was not available to report.
Xu F., Wu Y., Zhang C., Davis K.M., Moon K., Bushin L.B, & Seyedsayamdost M.R. (2019). A Genetics-Free Method for High-Throughput Discovery of Cryptic Microbial Metabolites. Nature chemical biology, 15(2), 161-168.
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