Extended Data Table 1.
16S rDNA analysis of fecal samples from two facilities identified discriminant biomarkers between IgA-High and IgA-Low samples.
| All Sample Comparison |
Facility 1 Comparison |
Facility 2 Comparison |
|||||||
|---|---|---|---|---|---|---|---|---|---|
| LDA Effect Size | LDA Effect Size | LDA Effect Size | |||||||
| Discriminant Biomarker | (log 10) | P-value | IgA | (log 10) | P-value | IgA | (log 10) | P-value | IgA |
| Proteobacteria.Betaproteobacteria | 3.37952 | 4.28E-17 | Low | 3.35270 | 0.004907 | Low | 3.43121 | 1.9E-15 | Low |
| Proteobacteria.Betaproteobacteria.Burkholderiales.Alcaligenaceae.Sutterella | 3.35757 | 4.28E-17 | Low | 3.35295 | 0.004907 | Low | 3.39543 | 1.9E-15 | Low |
| Bacteroidetes.Bacteroidia.Bacteroidales.Bacteroidaceae | 3.81243 | 0.003826 | High | 3.46226 | 7.65E-05 | Low | |||
| Bacteroidetes.Bacteroidia.Bacteroidales.Bacteroidaceae.Bacteroides | 3.81243 | 0.003826 | High | 3.45972 | 7.65E-05 | Low | |||
| Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae.Prevotella | 3.46939 | 0.008456 | High | 3.94783 | 6.31E-16 | Low | |||
| Bacteroidetes.Bacteroidia.Bacteroidales.Rikenellaceae | 3.72308 | 0.015021 | High | 3.82644 | 1.56E-12 | Low | |||
| Bacteroidetes.Bacteroidia.Bacteroidales | 3.20353 | 0.009979 | High | 3.13301 | 1.6E-12 | Low | |||
| Firmicutes.Clostridia.Clostridiales.Christensenellaceae | 3.53769 | 0.016585 | High | 3.33080 | 0.036190 | Low | |||
| Actinobacteria.Coriobacteriia.Coriobacteriales.Coriobacteriaceae | 3.22514 | 0.044352 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Paraprevotellaceae | 3.67592 | 9.65E-05 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Paraprevotellaceae.Prevotella | 3.67592 | 9.65E-05 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Prevotellaceae | 3.82596 | 9.65E-05 | Low | ||||||
| Deferribacteres | 3.35837 | 0.005758 | Low | ||||||
| Deferribacteres.Deferribacteres | 3.35874 | 0.005758 | Low | ||||||
| Deferribacteres.Deferribacteres.Deferribacterales | 3.36137 | 0.005758 | Low | ||||||
| Deferribacteres.Deferribacteres.Deferribacterales.Deferribacteracea | 3.35772 | 0.005758 | Low | ||||||
| Deferribacteres.Deferribacteres.Deferribacterales.Deferribacteraceae.Mucispirillum | 3.36082 | 0.005758 | Low | ||||||
| Proteobacteria.Gammaproteobacteria | 3.30927 | 0.019810 | Low | ||||||
| Proteobacteria.Gammaproteobacteria.Enterobacteriales | 3.30713 | 0.019810 | Low | ||||||
| Proteobacteria.Gammaproteobacteria.Enterobacteriales.Enterobacteriaceae | 3.31707 | 0.019810 | Low | ||||||
| Firmicutes.Clostridia.Clostridiales | 4.57889 | 0.000680 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Lachnospiraceae | 3.82545 | 0.017366 | High | ||||||
| Firmicutes.Clostridia.Clostridials.Lachnospiraceae.Dorea | 3.31929 | 0.026676 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Ruminococcaceae.Oscillospira | 3.84527 | 0.006447 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Ruminococcaceae.Ruminococcus | 3.77812 | 0.000499 | High | ||||||
| Proteobacteria.Alphaproteobacteria.RF32 | 3.27961 | 0.008611 | High | ||||||
| Proteobacteria.Epsilonproteobacteria.Campylobacterales.Helicobacteraceae | 3.62530 | 0.000393 | High | ||||||
| Tenericutes | 3.27403 | 0.001065 | High | ||||||
| Tenericutes.Mollicutes | 3.25535 | 0.003120 | High | ||||||
| Tenericutes.Mollicutes.RF39 | 3.25409 | 0.003120 | High | ||||||
| Bacteroidetes | 4.70727 | 0.000397 | Low | ||||||
| Bacteroidetes.Bacteroidia | 4.70727 | 0.000397 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Odoribacteraceae | 3.41723 | 1.22E-18 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Odoribacteraceae.Odoribacter | 3.47274 | 1.22E-18 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Porphyromonadaceae | 3.11464 | 0.000676 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.Porphyromonadaceae.Parabacteroides | 3.06586 | 0.000676 | Low | ||||||
| Bacteroidetes.Bacteroidia.Bacteroidales.S24_7 | 4.49336 | 0.034288 | Low | ||||||
| Firmicutes.Clostridia.Clostridials.Dehalobacteriaceae | 3.44482 | 0.010761 | Low | ||||||
| Firmicutes.Clostridia.Clostridials.Dehalobacteriaceae.Dehalobacterium | 3.45906 | 0.010761 | Low | ||||||
| Proteobacteria | 3.38346 | 8.98E-13 | Low | ||||||
| TM7 | 3.94808 | 0.013973 | Low | ||||||
| TM7.TM7_3 | 3.79262 | 0.013973 | Low | ||||||
| TM7.TM7 3.CW040 | 3.60561 | 0.013973 | Low | ||||||
| TM7.TM7_3.CW040.F16 | 3.84749 | 0.013973 | Low | ||||||
| Cyanobacteria | 3.19671 | 0.000962 | High | ||||||
| Cyanobacteria.4C0d_2 | 3.38513 | 0.001431 | High | ||||||
| Cyanobacteria.4C0d_2.YS2 | 3.31490 | 0.001431 | High | ||||||
| Firmicutes | 4.64404 | 0.003823 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Clostridiaceae | 3.92271 | 2.01 E-05 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Clostridiaceae.02d06 | 2.56784 | 0.024838 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Clostridiaceae.Clostridium | 2.54472 | 0.019193 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Clostridiaceae.Sarcina | 2.56391 | 0.021179 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Peptococcaceae.rc4_4 | 3.26329 | 0.000457 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Peptostreptococcaceae | 2.74377 | 0.034900 | High | ||||||
| Firmicutes.Clostridia.Clostridiales.Ruminococcaceae | 3.68674 | 0.000262 | High | ||||||
| Firmicutes.Erysipelotrichi.Erysipelotrichales.Erysipelotrichaceae | 2.56710 | 0.014173 | High | ||||||
| Tenericutes.Mollicutes.Anaeroplasmatales | 3.43058 | 0.012537 | High | ||||||
| Tenericutes.Mollicutes.Anaeroplasmatales.Anaeroplasmataceae | 3.41372 | 0.012537 | High | ||||||
| Tenericutes.Mollicutes.Anaeroplasmatales.Anaeroplasmataceae.Anaeroplasma | 3.43713 | 0.012537 | High | ||||||
The relative abundance of operational taxonomic units from 16S rDNA amplification of fecal sample DNA was determined with QIIME, and these data were input into LEfSe31 to identify discriminant biomarkers. After Kruskal-Wallis analysis (with an alpha-value of 0.05) of all features, a Linear Discriminant Analysis (LDA) model was used to rank discriminant features by the effect size with which they differentiate classes, in this case IgA-High versus IgA-Low samples. Analysis was performed to discriminate between IgA-High and IgA-Low samples from both facilities (“All Sample Comparison”), from Facility 1 only (“Facility 1 Comparison”) or Facility 2 only (“Facility 2 Comparison”). Biomarkers are depicted as Phylum.Class.Order.Family.Genus, to the level to which the taxonomic units were assignable by QIIME. “IgA” indicates whether the biomarker is enriched in IgA-High samples (“High”) or IgA-Low samples (“Low”).