Modular TaxSEA implementation supporting enrichment (KS) and
ORA (Fisher).
Provide either taxon_ranks for enrichment or
input_taxa for ORA.
Usage
TaxSEA(
taxon_ranks = NULL,
input_taxa = NULL,
mode = NULL,
lookup_missing = FALSE,
min_set_size = 5,
max_set_size = 300,
custom_db = NULL,
bugsigdb = FALSE
)Arguments
- taxon_ranks
Named numeric vector of statistics (e.g., log2 fold changes). Required for enrichment.
- input_taxa
Character vector of taxa to treat as "hits"/selected taxa. Required for ORA.
- mode
Character. One of
"enrichment"or"ora". If NULL, inferred from which input is provided.- lookup_missing
Logical indicating whether to fetch missing NCBI IDs. Default is FALSE.
- min_set_size
Minimum size of taxon sets to include in the analysis. Default is 5.
- max_set_size
Maximum size of taxon sets to include in the analysis. Default is 300.
- custom_db
A user-provided list of taxon sets. If NULL (default), the built-in database is used.
- bugsigdb
Logical; whether to augment the built-in database with BugSigDB signatures, which are downloaded (and cached) at run time via
bugsigdbr. Default is FALSE. Each set is tested against all the other taxa covered by the sets being analysed, and BugSigDB adds many extra taxa, so including it changes the p-values of every set, not only the BugSigDB ones. BugSigDB is also updated independently of TaxSEA. Set to TRUE to include it, and record the BugSigDB version used. If the download fails, a warning is given and the analysis continues without BugSigDB. Ignored whencustom_dbis supplied.
Examples
data("TaxSEA_test_data")
res <- TaxSEA(taxon_ranks = TaxSEA_test_data)
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
head(res$All_databases)
#> taxonSetName median_rank_of_set_members
#> 1 GMRepoV2_Decreased_in_Liver_Cirrhosis -3.6435
#> 2 mBodyMap_Oral 1.7750
#> 3 BacDive_Uses_nitrate_reduction 1.7750
#> 4 GMRepoV2_Decreased_in_Inflammatory_Bowel_Diseases -3.3870
#> 5 BloSSUM_taxa_Carter2023 -2.8795
#> 6 GMRepoV2_Increased_in_Inflammatory_Bowel_Diseases 1.4650
#> PValue Test_statistic FDR
#> 1 4.159210e-06 0.4534706 0.001301833
#> 2 1.568875e-05 0.7028986 0.002455290
#> 3 5.374713e-05 0.6259755 0.005607617
#> 4 9.592476e-05 0.4666667 0.007506113
#> 5 3.163143e-04 0.3878943 0.015138713
#> 6 3.607350e-04 0.4107946 0.015138713
#> TaxonSet
#> 1 Faecalibacterium_prausnitzii, Bacteroides_uniformis, Roseburia_hominis, Alistipes_putredinis, Bacteroides_dorei, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Bacteroides_faecis, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Bacteroides_xylanisolvens, Collinsella_aerofaciens, Bacteroides_massiliensis, Odoribacter_splanchnicus, Eubacterium_hallii, Bilophila_wadsworthia, Eubacterium_ramulus, Eubacterium_ventriosum, Coprococcus_catus, Alistipes_shahii, Roseburia_intestinalis, Eubacterium_siraeum, Intestinibacter_bartlettii, Ruminococcus_bromii, Bifidobacterium_adolescentis, Coprococcus_comes, Bacteroides_cellulosilyticus, Ruminococcus_callidus, Coprococcus_eutactus, Ruminococcus_lactaris, Bacteroides_finegoldii, Barnesiella_intestinihominis, Alistipes_indistinctus, Alistipes_onderdonkii, Bacteroides_intestinalis
#> 2 Streptococcus_salivarius, Haemophilus_parainfluenzae, Streptococcus_parasanguinis, Actinomyces_oris, Veillonella_parvula, Veillonella_dispar, Streptococcus_mitis, Streptococcus_sanguinis, Rothia_mucilaginosa, Actinomyces_sp_HPA0247, Actinomyces_sp_ICM47
#> 3 Escherichia_coli, Haemophilus_parainfluenzae, Clostridium_lavalense, Hungatella_hathewayi, Clostridium_bolteae, Actinomyces_oris, Veillonella_parvula, Veillonella_dispar, Veillonella_infantium, Veillonella_atypica, Rothia_mucilaginosa, Klebsiella_pneumoniae, Clostridium_saccharolyticum
#> 4 Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Akkermansia_muciniphila, Bacteroides_ovatus, Bacteroides_faecis, Dorea_formicigenerans, Roseburia_inulinivorans, Bacteroides_caccae, Collinsella_aerofaciens, Alistipes_finegoldii, Bacteroides_massiliensis, Odoribacter_splanchnicus, Eubacterium_ramulus, Adlercreutzia_equolifaciens, Coprococcus_catus, Clostridium_leptum, Parabacteroides_merdae, Ruminococcus_bromii, Ruminococcus_torques, Dialister_invisus, Bacteroides_fragilis, Alistipes_onderdonkii, Bacteroides_intestinalis
#> 5 Bacteroides_uniformis, Alistipes_putredinis, Bacteroides_dorei, Eubacterium_rectale, Anaerostipes_hadrus, Akkermansia_muciniphila, Bacteroides_ovatus, Bacteroides_faecis, Parasutterella_excrementihominis, Bacteroides_xylanisolvens, Bacteroides_caccae, Parabacteroides_distasonis, Alistipes_finegoldii, Bacteroides_massiliensis, Odoribacter_splanchnicus, Bacteroides_thetaiotaomicron, Bilophila_wadsworthia, Phascolarctobacterium_faecium, Lawsonibacter_asaccharolyticus, Alistipes_shahii, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Streptococcus_thermophilus, Parabacteroides_merdae, Bacteroides_stercoris, Bifidobacterium_adolescentis, Bifidobacterium_bifidum, Ruminococcus_torques, Bacteroides_cellulosilyticus, Ruminococcus_lactaris, Bacteroides_finegoldii, Barnesiella_intestinihominis, Alistipes_indistinctus, Alistipes_onderdonkii
#> 6 Anaerostipes_hadrus, Bacteroides_thetaiotaomicron, Streptococcus_salivarius, Bilophila_wadsworthia, Escherichia_coli, Gordonibacter_pamelaeae, Flavonifractor_plautii, Streptococcus_parasanguinis, Streptococcus_thermophilus, Eggerthella_lenta, Hungatella_hathewayi, Blautia_producta, Bifidobacterium_bifidum, Lactococcus_lactis, Ruminococcus_callidus, Veillonella_parvula, Clostridium_spiroforme, Bifidobacterium_dentium, Clostridium_scindens, Streptococcus_mitis, Rothia_mucilaginosa, Butyricicoccus_pullicaecorum, Bifidobacterium_animalis, Bifidobacterium_breve, Tyzzerella_nexilis, Ruminococcaceae_bacterium_D16, Enterococcus_faecium, Streptococcus_vestibularis, Anaerostipes_caccae
# \donttest{
# Include BugSigDB signatures (downloaded at run time)
res_bsdb <- TaxSEA(taxon_ranks = TaxSEA_test_data, bugsigdb = TRUE)
#>
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
#> Warning: p-value will be approximate in the presence of ties
head(res_bsdb$BugSigDB)
#> PubMedID
#> 1 39237540
#> 2 39237540
#> 3 39237540
#> 4 39237540
#> 5 35692191
#> 6 38968070
#> BugSigDB_ID
#> 1 bsdb_bsdb:39237540/12/2_Aging:All-cohorts-(Increased-age-group)_vs_All-cohorts-(Decreased-age-group)_DOWN
#> 2 bsdb_bsdb:39237540/13/2_Aging:All-cohorts-(Increased-age-group)_vs_All-cohorts-(Decreased-age-group)_DOWN
#> 3 bsdb_bsdb:39237540/15/2_Aging:All-cohorts-(Increased-age-group)_vs_All-Cohorts-(Decreasing-age-group)_DOWN
#> 4 bsdb_bsdb:39237540/4/2_Aging:All-Cohorts-(Increased-age-group)_vs_All-Cohorts-(Decreased-age-group)_DOWN
#> 5 bsdb_bsdb:35692191/2/2_Crohn's-disease:Crohn's-disease-patient_vs_Healthy-control-individual_DOWN
#> 6 bsdb_bsdb:38968070/11/1_Socioeconomic-status:Subjects-from-the-wealthier-households-based-on-economic-factors_vs_Subjects-from-the-least-well-off-households-based-on-economic-factors_UP
#> median_rank_of_set_members PValue Test_statistic FDR
#> 1 -3.753 6.403851e-06 0.5809088 0.0006774738
#> 2 -3.753 6.403851e-06 0.5809088 0.0006774738
#> 3 -3.753 6.403851e-06 0.5809088 0.0006774738
#> 4 -3.824 7.742558e-06 0.5426313 0.0006774738
#> 5 -4.711 4.351745e-05 0.7639752 0.0030462214
#> 6 -2.893 6.938443e-05 0.4099379 0.0037779329
#> TaxonSet
#> 1 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
#> 2 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
#> 3 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
#> 4 Faecalibacterium_prausnitzii, Roseburia_hominis, Eubacterium_rectale, Ruminococcus_gnavus, Dorea_longicatena, Blautia_obeum, Eubacterium_eligens, Dorea_formicigenerans, Roseburia_inulinivorans, Parasutterella_excrementihominis, Collinsella_aerofaciens, Eubacterium_hallii, Eubacterium_ventriosum, Coprococcus_catus, Roseburia_intestinalis, Bifidobacterium_pseudocatenulatum, Ruminococcus_bromii, Bifidobacterium_adolescentis, Coprococcus_comes, Ruminococcus_torques, Ruminococcus_callidus, Ruminococcus_lactaris
#> 5 Faecalibacterium_prausnitzii, Alistipes_putredinis, Dorea_longicatena, Roseburia_inulinivorans, Collinsella_aerofaciens, Eubacterium_siraeum, Parabacteroides_merdae, Ruminococcus_bromii
#> 6 Bacteroides_uniformis, Alistipes_putredinis, Bacteroides_dorei, Fusicatenibacter_saccharivorans, Blautia_wexlerae, Akkermansia_muciniphila, Bacteroides_ovatus, Dorea_formicigenerans, Roseburia_inulinivorans, Bacteroides_xylanisolvens, Bacteroides_caccae, Parabacteroides_distasonis, Collinsella_aerofaciens, Alistipes_finegoldii, Bacteroides_massiliensis, Odoribacter_splanchnicus, Bacteroides_thetaiotaomicron, Bilophila_wadsworthia, Phascolarctobacterium_faecium, Flavonifractor_plautii, Alistipes_shahii, Bacteroides_vulgatus, Bifidobacterium_longum, Parabacteroides_merdae, Bacteroides_stercoris, Ruminococcus_torques, Bacteroides_cellulosilyticus, Lactococcus_lactis, Coprococcus_eutactus, Ruminococcus_lactaris, Bacteroides_fragilis, Bacteroides_finegoldii, Barnesiella_intestinihominis, Alistipes_onderdonkii, Bacteroides_intestinalis
#> PubMedID.1
#> 1 39237540
#> 2 39237540
#> 3 39237540
#> 4 39237540
#> 5 35692191
#> 6 38968070
# }
# ORA example (toy): treat taxa with positive values as "hits"
hits <- names(TaxSEA_test_data)
res_ora <- TaxSEA(input_taxa = hits, mode = "ora")
head(res_ora$All_databases)
#> taxonSetName PValue
#> 1 Valles-Colomer2019_MGB006.Glutamate.synthesis.I 7.442269e-62
#> 2 Valles-Colomer2019_MGB007.Glutamate.synthesis.II 1.065220e-61
#> 3 Valles-Colomer2019_MGB029.ClpB.(ATP-dependent.chaperone.protein) 1.383936e-60
#> 4 Valles-Colomer2019_MGB036.S-Adenosylmethionine.(SAM).synthesis 3.382557e-60
#> 5 Valles-Colomer2019_MGB043.Acetate.synthesis.I 2.852085e-59
#> 6 Valles-Colomer2019_MGB033.Quinolinic.acid.degradation 1.052201e-57
#> Odds_ratio FDR
#> 1 45.11695 7.046430e-59
#> 2 44.78065 7.046430e-59
#> 3 38.35351 6.103159e-58
#> 4 37.69384 1.118781e-57
#> 5 38.52611 7.546618e-57
#> 6 35.83523 2.320103e-55
#> TaxonSet
#> 1 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Enterococcus_faecium, Gordonibacter_pamelaeae, Clostridium_citroniae, Dialister_succinatiphilus, Paraprevotella_clara, Lactobacillus_ruminis, Clostridium_leptum, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Odoribacter_laneus, Megamonas_hypermegale, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Alistipes_shahii, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Oxalobacter_formigenes, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Bacteroides_ovatus, Megamonas_funiformis, Methanobrevibacter_smithii, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Clostridium_asparagiforme, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Enterobacter_cloacae, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Enterococcus_faecalis, Streptococcus_infantarius, Streptococcus_anginosus, Lactobacillus_salivarius, Ruminococcus_gnavus, Fusobacterium_ulcerans, Clostridium_orbiscindens, Bifidobacterium_animalis, Mitsuokella_multacida, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lacticaseibacillus_rhamnosus, Pseudoflavonifractor_capillosus, Pseudomonas_sp., Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Veillonella_sp., Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Escherichia_sp., Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Neisseria_macacae, Acinetobacter_baumannii, Campylobacter_hominis, Enterococcus_saccharolyticus, Campylobacter_curvus, Campylobacter_concisus, Helicobacter_pylori, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Helicobacter_bilis, Providencia_stuartii, Listeria_grayi, Lactobacillus_brevis, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Corynebacterium_ammoniagenes, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Enterobacter_cancerogenus, 1872444, Paenibacillus_sp., NA, NA, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, 1872530, Bifidobacterium_sp., NA, 205, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, Helicobacter bizzozeronii, Helicobacter_canadensis, Helicobacter_cinaedi, Helicobacter_pullorum, Helicobacter_winghamensis, 576, Methanosphaera_stadtmanae, Providencia_alcalifaciens, 625, Streptococcus_sp., Victivallis_vadensis, Anaerofustis_stercorihominis, NA, Eubacterium_sp., Fusobacterium_necrophorum, 1977903, Weissella_paramesenteroides
#> 2 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Clostridium_citroniae, Dialister_succinatiphilus, Sutterella_wadsworthensis, Paraprevotella_clara, Lactobacillus_ruminis, Parasutterella_excrementihominis, Clostridium_leptum, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Megamonas_hypermegale, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Oxalobacter_formigenes, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Anaerotruncus_colihominis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Acidaminococcus_intestini, Turicibacter_sanguinis, Bacteroides_ovatus, Megamonas_funiformis, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Clostridium_asparagiforme, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Clostridium_difficile, Lactobacillus_fermentum, Fusobacterium_varium, Enterococcus_faecalis, Streptococcus_infantarius, Ruminococcus_gnavus, Clostridium_orbiscindens, Bifidobacterium_animalis, Mitsuokella_multacida, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lacticaseibacillus_rhamnosus, Pseudoflavonifractor_capillosus, Pseudomonas_sp., Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Clostridium_sporogenes, Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Veillonella_sp., Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Bacillus_sp., Enterococcus_sp., Escherichia_sp., Anaerococcus_hydrogenalis, Proteus_penneri, Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Acinetobacter_baumannii, Bacillus_cereus, Enterococcus_saccharolyticus, Campylobacter_jejuni, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Providencia_stuartii, Listeria_grayi, Lactobacillus_buchneri, Lactobacillus_brevis, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Grimontia_hollisae, Clostridium_hiranonis, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Burkholderiales_bacterium, Enterobacter_cancerogenus, 1872444, Bacillus smithii, Paenibacillus_sp., NA, NA, Vibrio_cholerae, 678, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, 1872530, Bifidobacterium_sp., NA, Campylobacter_coli, Campylobacter_upsaliensis, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, 576, NA, Providencia_alcalifaciens, 625, Victivallis_vadensis, Anaerofustis_stercorihominis, NA, Eubacterium_sp., 1977903, Fusobacterium_gonidiaformans, NA
#> 3 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Enterococcus_faecium, Gordonibacter_pamelaeae, Clostridium_citroniae, Dialister_succinatiphilus, Sutterella_wadsworthensis, Paraprevotella_clara, Lactobacillus_ruminis, Lactobacillus_crispatus, Parasutterella_excrementihominis, Clostridium_leptum, Limosilactobacillus_reuteri, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Odoribacter_laneus, Megamonas_hypermegale, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Alistipes_shahii, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Oxalobacter_formigenes, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Anaerotruncus_colihominis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Acidaminococcus_intestini, Turicibacter_sanguinis, Bacteroides_ovatus, Megamonas_funiformis, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Clostridium_asparagiforme, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Enterobacter_cloacae, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Clostridium_difficile, Lactobacillus_delbrueckii, Lactobacillus_johnsonii, Lactobacillus_fermentum, Lactobacillus_gasseri, Fusobacterium_varium, Enterococcus_faecalis, Streptococcus_infantarius, Streptococcus_anginosus, Lactobacillus_salivarius, Ruminococcus_gnavus, Fusobacterium_ulcerans, Clostridium_orbiscindens, Bifidobacterium_animalis, Mitsuokella_multacida, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lactobacillus_acidophilus, Lacticaseibacillus_rhamnosus, Pediococcus_acidilactici, Pseudoflavonifractor_capillosus, Pseudomonas_sp., Sutterella_parvirubra, Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Clostridium_sporogenes, Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Finegoldia_magna, Veillonella_sp., Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Bacillus_sp., Enterococcus_sp., Escherichia_sp., Anaerococcus_hydrogenalis, Proteus_penneri, Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Neisseria_macacae, Acinetobacter_baumannii, Bacillus_cereus, Campylobacter_hominis, Enterococcus_saccharolyticus, Campylobacter_jejuni, Campylobacter_curvus, Campylobacter_concisus, Helicobacter_pylori, Lactobacillus_helveticus, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Helicobacter_bilis, Providencia_stuartii, Listeria_grayi, Lactobacillus_buchneri, Lactobacillus_brevis, Lactobacillus_antri, Leuconostoc_mesenteroides, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Grimontia_hollisae, Corynebacterium_ammoniagenes, Clostridium_hiranonis, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Lactobacillus_amylolyticus, Lactobacillus_ultunensis, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Burkholderiales_bacterium, Enterobacter_cancerogenus, 1872444, Bacillus smithii, Paenibacillus_sp., NA, NA, Vibrio_cholerae, 678, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, NA, 1872530, Bifidobacterium_sp., NA, Campylobacter_coli, 205, Campylobacter_upsaliensis, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, Helicobacter bizzozeronii, Helicobacter_canadensis, Helicobacter_cinaedi, Helicobacter_pullorum, Helicobacter_winghamensis, 576, NA, Providencia_alcalifaciens, 625, Streptococcus_sp., Victivallis_vadensis, Anaerofustis_stercorihominis, Eubacterium_sp., Fusobacterium_necrophorum, 1977903, Weissella_paramesenteroides, Fusobacterium_gonidiaformans, NA, Lactobacillus_fructivorans, Parvimonas_micra, Bartonella_quintana, 1591
#> 4 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Enterococcus_faecium, Gordonibacter_pamelaeae, Clostridium_citroniae, Dialister_succinatiphilus, Sutterella_wadsworthensis, Paraprevotella_clara, Lactobacillus_ruminis, Lactobacillus_crispatus, Parasutterella_excrementihominis, Clostridium_leptum, Limosilactobacillus_reuteri, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Odoribacter_laneus, Megamonas_hypermegale, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Alistipes_shahii, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Oxalobacter_formigenes, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Anaerotruncus_colihominis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Acidaminococcus_intestini, Turicibacter_sanguinis, Bacteroides_ovatus, Megamonas_funiformis, Methanobrevibacter_smithii, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Clostridium_asparagiforme, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Enterobacter_cloacae, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Clostridium_difficile, Lactobacillus_delbrueckii, Lactobacillus_johnsonii, Lactobacillus_fermentum, Lactobacillus_gasseri, Fusobacterium_varium, Enterococcus_faecalis, Streptococcus_infantarius, Streptococcus_anginosus, Lactobacillus_salivarius, Ruminococcus_gnavus, Fusobacterium_ulcerans, Clostridium_orbiscindens, Bifidobacterium_animalis, Mitsuokella_multacida, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lactobacillus_acidophilus, Lacticaseibacillus_rhamnosus, Pediococcus_acidilactici, Pseudoflavonifractor_capillosus, Pseudomonas_sp., Sutterella_parvirubra, Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Clostridium_sporogenes, Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Finegoldia_magna, Veillonella_sp., Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Bacillus_sp., Enterococcus_sp., Escherichia_sp., Anaerococcus_hydrogenalis, Proteus_penneri, Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Neisseria_macacae, Acinetobacter_baumannii, Bacillus_cereus, Campylobacter_hominis, Enterococcus_saccharolyticus, Campylobacter_jejuni, Campylobacter_curvus, Campylobacter_concisus, Helicobacter_pylori, Lactobacillus_helveticus, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Helicobacter_bilis, Providencia_stuartii, Listeria_grayi, Lactobacillus_buchneri, Lactobacillus_brevis, Lactobacillus_antri, Leuconostoc_mesenteroides, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Grimontia_hollisae, Corynebacterium_ammoniagenes, Clostridium_hiranonis, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Lactobacillus_amylolyticus, Lactobacillus_ultunensis, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Burkholderiales_bacterium, Enterobacter_cancerogenus, 1872444, Bacillus smithii, Paenibacillus_sp., NA, NA, Vibrio_cholerae, 678, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, NA, 1872530, Bifidobacterium_sp., NA, Campylobacter_coli, 205, Campylobacter_upsaliensis, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, Helicobacter bizzozeronii, Helicobacter_canadensis, Helicobacter_cinaedi, Helicobacter_pullorum, Helicobacter_winghamensis, 576, Methanosphaera_stadtmanae, NA, Providencia_alcalifaciens, 625, Streptococcus_sp., Victivallis_vadensis, Anaerofustis_stercorihominis, NA, Eubacterium_sp., Fusobacterium_necrophorum, 1977903, Weissella_paramesenteroides, Fusobacterium_gonidiaformans, NA, Lactobacillus_fructivorans, Parvimonas_micra, Bartonella_quintana, 1591
#> 5 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Enterococcus_faecium, Clostridium_citroniae, Paraprevotella_clara, Lactobacillus_ruminis, Lactobacillus_crispatus, Clostridium_leptum, Limosilactobacillus_reuteri, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Odoribacter_laneus, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Alistipes_shahii, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Anaerotruncus_colihominis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Acidaminococcus_intestini, Turicibacter_sanguinis, Bacteroides_ovatus, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Clostridium_asparagiforme, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Enterobacter_cloacae, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Clostridium_difficile, Lactobacillus_delbrueckii, Lactobacillus_johnsonii, Lactobacillus_fermentum, Lactobacillus_gasseri, Fusobacterium_varium, Enterococcus_faecalis, Streptococcus_infantarius, Streptococcus_anginosus, Lactobacillus_salivarius, Ruminococcus_gnavus, Fusobacterium_ulcerans, Clostridium_orbiscindens, Bifidobacterium_animalis, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lactobacillus_acidophilus, Lacticaseibacillus_rhamnosus, Pediococcus_acidilactici, Pseudoflavonifractor_capillosus, Pseudomonas_sp., Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Clostridium_sporogenes, Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Finegoldia_magna, Veillonella_sp., Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Bacillus_sp., Escherichia_sp., Anaerococcus_hydrogenalis, Proteus_penneri, Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Neisseria_macacae, Acinetobacter_baumannii, Bacillus_cereus, Campylobacter_hominis, Enterococcus_saccharolyticus, Campylobacter_jejuni, Campylobacter_curvus, Campylobacter_concisus, Helicobacter_pylori, Lactobacillus_helveticus, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Providencia_stuartii, Listeria_grayi, Lactobacillus_buchneri, Lactobacillus_brevis, Lactobacillus_antri, Leuconostoc_mesenteroides, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Grimontia_hollisae, Corynebacterium_ammoniagenes, Clostridium_hiranonis, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Lactobacillus_amylolyticus, Lactobacillus_ultunensis, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Enterobacter_cancerogenus, 1872444, Paenibacillus_sp., NA, NA, Vibrio_cholerae, 678, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, NA, 1872530, Bifidobacterium_sp., NA, Campylobacter_coli, 205, Campylobacter_upsaliensis, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, Helicobacter bizzozeronii, Helicobacter_canadensis, Helicobacter_cinaedi, Helicobacter_pullorum, Helicobacter_winghamensis, 576, NA, Providencia_alcalifaciens, 625, Streptococcus_sp., Victivallis_vadensis, Anaerofustis_stercorihominis, NA, Eubacterium_sp., Fusobacterium_necrophorum, Weissella_paramesenteroides, Fusobacterium_gonidiaformans, NA, Lactobacillus_fructivorans, Parvimonas_micra, 1591
#> 6 Eubacterium_rectale, Bifidobacterium_stercoris, Bifidobacterium_longum, Eubacterium_eligens, Anaerobutyricum_hallii, Ruminococcus_obeum, Dorea_longicatena, Ruminococcus_torques, Coprococcus_comes, Dorea_formicigenerans, Bifidobacterium_catenulatum, Coprococcus_catus, Eubacterium_ventriosum, Intestinibacter_bartlettii, Enterococcus_faecium, Clostridium_citroniae, Dialister_succinatiphilus, Sutterella_wadsworthensis, Paraprevotella_clara, Lactobacillus_ruminis, Lactobacillus_crispatus, Parasutterella_excrementihominis, Clostridium_leptum, Limosilactobacillus_reuteri, Bacteroides_dorei, Bifidobacterium_breve, Bacteroides_caccae, Bacteroides_coprocola, Ruminococcus_lactaris, Parabacteroides_merdae, Veillonella_parvula, Bacteroides_finegoldii, Escherichia_coli, Bacteroides_coprophilus, Odoribacter_laneus, Megamonas_hypermegale, Desulfovibrio_piger, Paraprevotella_xylaniphila, Collinsella_intestinalis, Prevotella_copri, Bacteroides_vulgatus, Bacteroides_stercoris, Bacteroides_uniformis, Prevotella_stercorea, Roseburia_inulinivorans, Roseburia_intestinalis, Bacteroides_thetaiotaomicron, Bacteroides_intestinalis, Roseburia_hominis, Alistipes_shahii, Bifidobacterium_pseudocatenulatum, Bacteroides_xylanisolvens, Bacteroides_cellulosilyticus, Oxalobacter_formigenes, Blautia_producta, Bilophila_wadsworthia, Ruminococcus_bromii, Bifidobacterium_Bifidum, Coprococcus_eutactus, Clostridium_hathewayi, Tyzzerella_nexilis, Anaerotruncus_colihominis, Holdemania_filiformis, Alistipes_indistinctus, Collinsella_aerofaciens, Faecalibacterium_prausnitzii, Alistipes_putredinis, Collinsella_tanakaei, Bacteroides_eggerthii, Acidaminococcus_intestini, Turicibacter_sanguinis, Bacteroides_ovatus, Megamonas_funiformis, Methanobrevibacter_smithii, Butyrivibrio_crossotus, Bifidobacterium_angulatum, Parabacteroides_johnsonii, Eubacterium_siraeum, Citrobacter_freundii, Akkermansia_muciniphila, Bacteroides_fragilis, Odoribacter_splanchnicus, Bacteroides_plebeius, Bacteroides_clarus, Clostridium_symbiosum, Catenibacterium_mitsuokai, Bacteroides_distasonis, Fusobacterium_mortiferum, Enterobacter_cloacae, Megasphaera_elsdenii, Blautia_hydrogenotrophica, Bacteroides_fluxus, Bifidobacterium_dentium, Clostridium_bolteae , Clostridium_difficile, Lactobacillus_delbrueckii, Lactobacillus_johnsonii, Lactobacillus_fermentum, Lactobacillus_gasseri, Fusobacterium_varium, Enterococcus_faecalis, Streptococcus_infantarius, Streptococcus_anginosus, Lactobacillus_salivarius, Ruminococcus_gnavus, Fusobacterium_ulcerans, Clostridium_orbiscindens, Bifidobacterium_animalis, Mitsuokella_multacida, Blautia_hansenii, Lactobacillus_casei, Anaerostipes_caccae, Clostridium_scindens, Subdoligranulum_variabile, Clostridium_spiroforme, Collinsella_stercoris, Lactobacillus_acidophilus, Lacticaseibacillus_rhamnosus, Pediococcus_acidilactici, Pseudomonas_sp., Sutterella_parvirubra, Eggerthella._sp., Clostridium_sp., Subdoligranulum_sp., Clostridium_sporogenes, Succinatimonas_hippei, Butyrivibrio_fibrisolvens, Parabacteroides_sp., Lactobacillus_paracasei, Finegoldia_magna, Pseudomonas_aeruginosa, Ruminococcus_sp., Fusobacterium_sp., Bacteroides_sp., Bacillus_sp., Enterococcus_sp., Escherichia_sp., Anaerococcus_hydrogenalis, Proteus_penneri, Providencia_rettgeri, Edwardsiella_tarda, Acinetobacter_junii, Neisseria_macacae, Acinetobacter_baumannii, Bacillus_cereus, Campylobacter_hominis, Enterococcus_saccharolyticus, Campylobacter_jejuni, Campylobacter_curvus, Campylobacter_concisus, Helicobacter_pylori, Lactobacillus_helveticus, Listeria_monocytogenes, Porphyromonas_gingivalis, Yersinia_enterocolitica, Yersinia_pseudotuberculosis, Helicobacter_bilis, Providencia_stuartii, Listeria_grayi, Lactobacillus_buchneri, Lactobacillus_brevis, Lactobacillus_antri, Leuconostoc_mesenteroides, Streptococcus_equinus, Ruminococcaceae_bacterium, Laribacter_hongkongensis, Yersinia_bercovieri, Vibrio_mimicus, Vibrio_furnissii, Escherichia_albertii, Hafnia_alvei, Grimontia_hollisae, Corynebacterium_ammoniagenes, Clostridium_hiranonis, Lachnospiraceae_bacterium, Bifidobacterium_gallicum, Lactobacillus_amylolyticus, Lactobacillus_ultunensis, Marvinbryantia_formatexigens, Bacteroides_pectinophilus, Erysipelotrichaceae_bacterium, Prevotella_salivae, Clostridium_hylemonae, Citrobacter_koseri, Citrobacter_youngae, Enterobacteriaceae_bacterium, Lactobacillus_coryniformis, Arcobacter_butzleri, Burkholderiales_bacterium, Enterobacter_cancerogenus, 1872444, Bacillus smithii, Paenibacillus_sp., NA, NA, Vibrio_cholerae, 678, Burkholderia oklahomensis, Providencia_rustigianii, 54061, NA, NA, 1872530, Bifidobacterium_sp., NA, Campylobacter_coli, 205, Campylobacter_upsaliensis, 1896336, Clostridium_clostridioforme, Clostridium_methylpentosum, Coprobacillus_sp., 2049024, Desulfovibrio_sp., Dysgonomonas_mossii, Helicobacter bizzozeronii, Helicobacter_canadensis, Helicobacter_cinaedi, Helicobacter_pullorum, Helicobacter_winghamensis, 576, Methanosphaera_stadtmanae, NA, Providencia_alcalifaciens, 625, Streptococcus_sp., Victivallis_vadensis, Anaerofustis_stercorihominis, Eubacterium_sp., Fusobacterium_necrophorum, 1977903, Weissella_paramesenteroides, Fusobacterium_gonidiaformans, NA, Lactobacillus_fructivorans, Parvimonas_micra, Bartonella_quintana, 1591