Table 3. Median and range proportion of foals with sequences detected in the fecal DNA of rectal swab samples (Phylum, class, order, and family).
| Microbial Family | 2-day-old foals (N = 37) | 30-day-old foals (N = 37) | P* | |||
| Archaea.Euryarchaeota | 0% (0/37) | 35% (13/37) | 0.0117 | |||
| Methanobacteria | 0% (0/37) | 24% (9/37) | 0.0770 | |||
| Methanobacteriales | 0% (0/37) | 24% (9/37) | 0.1925 | |||
| Methanobacteriacae | 0% (0/37) | 24% (9/37) | 0.4851 | |||
| Methanomicrobia | 0% (0/37) | 16% (6/37) | 0.3708 | |||
| Methanomicrobiales | 0% (0/37) | 16% (6/37) | 0.9064 | |||
| Methanocorpusculaceae | 0% (0/37) | 16% (6/37) | 1.0000 | |||
| Bacteria.Acidobacteria | 0% (0/37) | 3% (1/37) | 0.9999 | |||
| Acidobacteria | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Acidobacteriales | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Acidobacteriaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Bacteria.Actinobacteria | 73% (27/37) | 97% (36/37) | 0.1590 | |||
| Actinobacteria | 73% (27/37) | 97% (36/37) | 0.1925 | |||
| Actinomycetales (order) | 62% (23/37) | 73% (27/37) | 1.0000 | |||
| Bifidobacteriales (order) | 3% (1/37) | 8% (3/37) | 1.0000 | |||
| Other | 14% (5/37) | 8% (3/37) | 1.0000 | |||
| Coriobacteridae (subclass) | 24% (9/37) | 76% (28/37) | 0.0041 | |||
| Coriobacteriales | 24% (9/37) | 76% (28/37) | 0.0221 | |||
| Rubrobacteridae (subclass) | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Rubrobacterales | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Other order | 0% (0/37) | 27% (10/37) | 0.1452 | |||
| Other family | 0% (0/37) | 27% (10/37) | 0.2944 | |||
| Bacteria.Bacteroidetes | 92% (34/37) | 100% (37/37) | 0.5152 | |||
| Bacteroidetes | 89% (33/37) | 100% (37/37) | 1.0000 | |||
| Bacteroidales | 89% (33/37) | 100% (37/37) | 1.0000 | |||
| Bacteroidieacae | 86% (32/37) | 95% (35/37) | 1.0000 | |||
| Porphyromonadaceae | 30% (11/37) | 89% (33/37) | <0.0001 | |||
| Prevotellaceae | 8% (3/37) | 95% (35/37) | <0.0001 | |||
| Rikenellaceae | 11% (4/37) | 49% (18/37) | 0.1496 | |||
| Other | 11% (4/37) | 95% (35/37) | <0.0001 | |||
| Flavobacteria | 16% (6/37) | 11% (4/37) | 1.0000 | |||
| Flavobacteriales | 16% (6/37) | 11% (4/37) | 1.0000 | |||
| Flavobacteriaceae | 16% (6/37) | 11% (4/37) | 1.0000 | |||
| Sphingobacteria | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Sphingobacteriales | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Crenotrichaceae | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Flexibacteriaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Sphingobacteriaceae | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Other class | 27% (10/37) | 95% (35/37) | <0.0001 | |||
| Other order | 27% (10/37) | 95% (35/37) | <0.0001 | |||
| Other family | 27% (10/37) | 95% (35/37) | <0.0001 | |||
| Bacteria.Chlamydiae | 0% (0/37) | 51% (19/37) | <0.0001 | |||
| Chlamydiae | 0% (0/37) | 51% (19/37) | <0.0001 | |||
| Chlamydiales | 0% (0%) | 51% (19/37) | <0.0001 | |||
| Chlamydiaceae | 0% (0%) | 51% (19/37) | <0.0001 | |||
| Parachlamydiaceae | 0% (0%) | 3% (1/37) | 1.0000 | |||
| Bacteria.Chloroflexi | 0% (0/37) | 22% (8/37) | 0.1463 | |||
| Anaerolineae | 0% (0/37) | 22% (8/37) | 0.1173 | |||
| Caldilineae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Caldilineales | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Other | 0% (0/37) | 19% (7/37) | 0.7223 | |||
| Other family | 0% (0/37) | 19% (7/37) | 1.0000 | |||
| Bacteria.Cyanobacteria | 0% (0/37) | 3% (1/37) | 0.9999 | |||
| Cyanobacteria | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Other order | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Other family | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Bacteria.Deferribacteres | 3% (1/37) | 5% (2/37) | 0.9999 | |||
| Deferribacteres | 3% (1/37) | 5% (2/37) | 1.0000 | |||
| Deferribacterales | 3% (1/37) | 5% (2/37) | 1.0000 | |||
| Deferribacteraceae | 0% (0%) | 0% (0%) | NP | |||
| Incertae sedis 3 | 3% (1/37) | 5% (2/37) | 1.0000 | |||
| Bacteria.Fibrobacteres | 0% (0/37) | 14% (5/37) | 0.5152 | |||
| Fibrobacteres | 0% (0/37) | 14% (5/37) | 0.4698 | |||
| Fibrobacterales | 0% (0/37) | 14% (5/37) | 0.9515 | |||
| Fibrobacteraceae | 0% (0/37) | 14% (5/37) | 1.0000 | |||
| Bacteria.Firmicutes | 100% (37/37) | 100% (37/37) | NP | |||
| Bacilli | 100% (37/37) | 100% (37/37) | NP | |||
| Lactobacillales | 100% (37/37) | 100% (37/37) | NP | |||
| Aerococcaceae | 27% (10/37) | 14% (5/37) | 1.0000 | |||
| Carnobacteriaceae | 14% (5/37) | 3% (1/37) | 1.0000 | |||
| Enterococcaceae | 95% (35/37) | 41% (15/37) | 0.0078 | |||
| Lactobacillaceae | 27% (10/37) | 70% (26/37) | 0.2944 | |||
| Leuconostocaceae | 8% (3/37) | 0% (0/37) | 1.0000 | |||
| Streptococcaceae | 97% (36/37) | 97%(36/37) | 1.0000 | |||
| Other | 78% (29/37) | 22% (8/37) | <0.0001 | |||
| Bacillales | 46% (17/37) | 70% (26/37) | 1.0000 | |||
| Paenibacillaceae | 3% (1/37) | 5% (2/37) | 1.0000 | |||
| Staphylococcaceae | 32% (12/37) | 62% (23/37) | 1.0000 | |||
| Bacillaceae | 14% (5/37) | 14% (5/37) | 1.0000 | |||
| Incertae Sedis XI | 11% (4/37) | 3% (1/37) | 1.0000 | |||
| Planococcaceae | 3% (1/37) | 11% (4/37) | 1.0000 | |||
| Other | 0% (0/37) | 8% (3/37) | 1.0000 | |||
| Other order | 30% (11/37) | 11% (4/37) | 1.0000 | |||
| Other family | 30% (11/37) | 11% (4/37) | 1.0000 | |||
| Clostridia | 100% (37/37) | 100% (37/37) | NP | |||
| Clostridiales | 100% (37/37) | 100% (37/37) | NP | |||
| Eubacteriaceae | 5% (2/37) | 35% (13/37) | 0.6076 | |||
| Lachnospiraceae | 89% (33/37) | 100% (37/37) | 1.0000 | |||
| Peptostreptococcaceae | 43% (16/37) | 0.0150 | ||||
| Ruminococcaceae | 70% (26/37) | 100% (37/37) | 0.1716 | |||
| Clostridiaceae | 100% (37/37) | 78% (29/37) | 0.7980 | |||
| Incertae Sedis XI | 11% (4/37) | 78% (29/37) | <0.0001 | |||
| Incertae Sedis XIII | 5% (2/37) | 57% (21/37) | 0.0154 | |||
| Peptococcaceae | 0% (0/37) | 32% (12/37) | 0.1065 | |||
| Veillonellaceae | 16% (6/37) | 95% (35/37) | <0.0001 | |||
| Other | 100% (37/37) | 97% (36/37) | 1.0000 | |||
| Other order | 32% (12/37) | 59% (22/37) | 0.8136 | |||
| Other family | 32% (12/37) | 59% (22/37) | 1.0000 | |||
| Erysipelotrichi | 62% (23/37) | 70% (26/37) | 1.0000 | |||
| Erysipelotrichales | 62% (23/37) | 70% (26/37) | 1.0000 | |||
| Erysipelotrichiaceae | 62% (23/37) | 70% (26/37) | 1.0000 | |||
| Other class | 49% (18/37) | 86% (32/37) | 0.0242 | |||
| Other order | 49% (18/37) | 86% (32/37) | 0.0594 | |||
| Other family | 49% (18/37) | 86% (32/37) | 1.0000 | |||
| Bacteria.Fusobacteria | 62% (23/37) | 84% (31/37) | 0.5152 | |||
| Fusobacteria | 62% (23/37) | 84% (31/37) | 1.0000 | |||
| Fusobacteriales | 62% (23/37) | 84% (31/37) | 1.0000 | |||
| Fusobacteriaceae | 62% (23/37) | 81% (30/37) | 1.0000 | |||
| Incertae sedis 11 | 5% (2/37) | 0% (0/37) | 1.0000 | |||
| Other | 32% (12/37) | 43% (16/37) | 1.0000 | |||
| Bacteria.Lentisphaerae | 0% (0/37) | 0% (0/37) | NP | |||
| Lentisphaerae | 0% (0/37) | 0% (0/37) | NP | |||
| Victivallales | 0% (0/37) | 0% (0/37) | NP | |||
| Victivallaceae | 0% (0/37) | 0% (0/37) | NP | |||
| Bacteria.Other | 86% (32/37) | 100% (37/37) | 0.5152 | |||
| Bacteria. Other Class | 86% (32/37) | 100% (37/37) | 1.0000 | |||
| Other Order | 86% (32/37) | 100% (37/37) | 1.0000 | |||
| Other family | 86% (32/37) | 100% (37/37) | 1.0000 | |||
| Bacteria.Planctomycetes | 3% (1/37) | 43% (16/37) | 0.0045 | |||
| Planctomycetacia | 3% (1/37%) | 43% (16/37) | 0.0377 | |||
| Planctomycetales | 3% (1/37) | 43% (16/37) | 0.0120 | |||
| Planctomycetaceae | 3% (1/37) | 43% (16/37) | 0.0003 | |||
| Bacteria.Proteobacteria | 100% (37/37) | 97% (36/37) | 0.9999 | |||
| Alphaproteobacteria | 11% (4/37) | 14% (5/37) | 1.0000 | |||
| Caulobacterales | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Caulobacteriaceae | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Rhizobiales | 5% (2/37) | 8% (3/37) | 1.0000 | |||
| Hyphomicrobiaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Methylobacteriaceae | 3% (1/37) | 3% (1/37) | 1.0000 | |||
| Other | 3% (1/37) | 3% (1/37) | 1.0000 | |||
| Rhodobacteriales | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Rhodobacteriaceae | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Rhodospirales | 0% (0%) | 0% (0%) | NP | |||
| Other | 0% (0%) | 0% (0%) | NP | |||
| Other order | 0% (0%) | 3% (1/37) | 1.0000 | |||
| Other family | 0% (0%) | 3% (1/37) | 1.0000 | |||
| Betaproteobacteria | 11% (4/37) | 27% (10/37) | 1.0000 | |||
| Burkholderiales | 8% (3/37) | 24% (9/37%) | 1.0000 | |||
| Alcaligenaceae | 3% (1/37) | 3% (1/37) | 1.0000 | |||
| Comamonadacea | 3% (1/37) | 8% (3/37) | 1.0000 | |||
| Other | 3% (1/37) | 14% (5/37) | 1.0000 | |||
| Other order | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Other family | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Deltaproteobacteria | 5% (2/37) | 49% (18/37) | 0.0104 | |||
| Desulfovibrionales | 5% (2/37) | 46% (17/37) | 0.0377 | |||
| Desulfovibrionaceae | 5% (2/37) | 43% (16/37) | 0.1496 | |||
| Other | 3% (1/37) | 14% (5/37) | 1.0000 | |||
| Myxococcales | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Nannocystineae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Other | 0% (0/37) | 0% (0/37) | NP | |||
| Epsilonproteobacteria | 3% (1/37) | 73% (27/37) | <0.0001 | |||
| Campylobacterales | 3% (1/37) | 73% (27/37) | <0.0001 | |||
| Campylobacteriaceae | 3% (1/37) | 65% (24/37) | <0.0001 | |||
| Helicobacteraceae | 0% (0/37) | 43% (16/37) | 0.0154 | |||
| Gamma proteobacteria | 97% (36/37) | 89% (33/37) | 1.0000 | |||
| Aeromonadales | 22% (8/37) | 41% (15/37) | 1.0000 | |||
| Aeromonadaceae | 22% (8/37) | 0% (0/37) | 0.7980 | |||
| Succinivibrionaceae | 0% (0/37) | 41% (15/37) | 0.0219 | |||
| Enterobacteriales | 95% (35/37) | 62% (23/37) | 0.0858 | |||
| Enterobacteriaceae | 95% (35/37) | 62% (23/37) | 0.2145 | |||
| Legionellales | 0% (0/37) | 5% (2/37) | 1.0000 | |||
| Coxiellaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Legionellaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Oceanospirillales | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Halomonadaceae | 3% (1/37) | 0% (0/37) | 1.0000 | |||
| Pasteurellales | 32% (12/37) | 38% (14/37) | 1.0000 | |||
| Pasteurellaceae | 32% (12/37) | 38% (14/37) | 1.0000 | |||
| Pseudomonadales | 14% (5/37) | 11% (4/37) | 1.0000 | |||
| Moraxellaceae | 14% (5/37) | 11% (4/37) | 1.0000 | |||
| Pseudomonadaceae | 5% (2/37) | 3% (1/37) | 1.0000 | |||
| Xanthomonadales | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Xanthomonadaceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Other order | 16% (6/37) | 0% (0/37) | 0.9064 | |||
| Other family | 16% (6/37) | 0% (0/37) | 1.0000 | |||
| Other class | 5% (2/37) | 43% (16/37) | 0.0242 | |||
| Other order | 5% (2/37) | 43% (16/37) | 0.0594 | |||
| Other family | 5% (2/37) | 43% (16/37) | 0.1496 | |||
| Bacteria.Spirochaetes | 0% (0/37) | 30% (11/37) | 0.0312 | |||
| Spirochaetes | 0% (0/37) | 30% (11/37) | 0.0439 | |||
| Spirochaetales | 0% (0/37) | 30% (11/37) | 0.0910 | |||
| Spirochaetaceae | 0% (0/37) | 30% (11/37) | 0.1716 | |||
| Other | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Bacteria.TM7 | 0% (0/37) | 35% (13/37) | 0.0117 | |||
| TM7 genera incertae sedis | 0% (0/37) | 35% (13/37) | 0.0218 | |||
| Other order | 0% (0/37) | 35% (13/37) | 0.0351 | |||
| Other family | 0% (0/37) | 35% (13/37) | 0.0648 | |||
| Bacteria.Tenericutes | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Mollicutes | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Anaeroplasmatales | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Anaeroplasmataceae | 0% (0/37) | 3% (1/37) | 1.0000 | |||
| Bacteria.Verrucomicrobia | 24% (9/37) | 89% (33/37) | <0.0001 | |||
| Verrucomicrobiae | 24% (9/37) | 89% (33/37) | <0.0001 | |||
| Verrucomicrobiales | 24% (9/37) | 89% (33/37) | <0.0001 | |||
| Other | 0% (0%) | 5% (2/37) | 1.0000 | |||
| Subdivision 5 | 8% (3/37) | 76% (28/37) | <0.0001 | |||
| Verrucomicrobiaceae | 16% (6/37) | 78% (29/37) | <0.0001 | |||
| Xiphinematobacteriaceae | 0% (0%) | 3% (1/37) | 1.0000 | |||
| Other Kingdom, Other phylum | 19% (7/37) | 22% (8/37) | 0.9999 | |||
| Other class | 19% (7/37) | 22% (8/37) | 1.0000 | |||
| Other order | 19% (7/37) | 22% (8/37) | 1.0000 | |||
| Other family | 19% (7/37) | 22% (8/37) | 1.0000 | |||
Fecal swab samples collected from 37 Quarter Horse foals on days 2 and 30 of life. *P values represent the results of McNemar’s test for paired dichotomous data, adjusted by the method of Hochberg. NP = Not Performed.