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Bacterial Vaginosis STI Compositional Subtype Biomarkers Classification

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) - iners L. PICRUSt Negative Intermediate no yes C1 C2 C3 no.cluster TP TN FP FN 3.26 0.27 Positive STI Compositional.subtype Cytokine_biomarkers alpha_diversity BV (not vaginosis Positive Negative Intermediate no yes C1 C2 C3 no.cluster TP TN FP FN 3.26 0.27 STI Compositional.subtype Cytokine_biomarkers alpha_diversity BV Relative abundance True Positive True Negative True FalsePositive FalseNegative C1 C2 C3 No cluster Positive (Nugent7-10) Negative (Nugent 0-3) Intermediate (Nugent 4-6) 10 5 0 15 Positive Negative 0.27 Positive Negative Intermediate no yes C1 C2 C3 no.cluster TP TN FP FN 3.26 10 5 0 15 BV STI Compositional.subtype Cytokine_biomarkers alpha_diversity Compositional subtype Compositional Biomarkersclassification diversityAlpha Bacterial STI Lactobacillus 045 − 68 − D.propionicifaciens Peptoniphilus C.ureolyticus A.hydrogenalis C.amycolatum_lactis Corynebacterium P.bennonis ph2 P.coxii C.hominis Porphyromonas M.curtisii Finegoldia P.corporis B.coagulans Peptostreptococcaceae Dialister C.glucuronolyticum P.niger V.cambriense Clostridium Enterobacteriaceae Staphylococcus C.tuberculostearicum F.nucleatum WAL_1855D Anaerococcus P.harei_asaccharolyticus_grossensis F.magna P.buccalis A.prevotii_tetradius P.eunonis P.lacrimalis P.bivia P.disiens M.mulieris P.anaerobius F.equinum U.parvum_urealyticum A.radingae P.harei_gorbachii P.bergensis Sutterella [Mogibacteriaceae] P.somerae Desulfovibrio M.morganii Porphyromonadaceae Clostridiales P.stomatis Moryella M.spermatophilum Campylobacter Bacteroidales S.infantis_mitis_oralis S.salivarius_thermophilus_vestibularis C.coyleae_mucifaciens C.imitans F.hominis A.octavius C.thomssenii_sundsvallense Micrococcus C.urealyticum C.tuscaniense Gallicola 1 J.anthropi Jeotgalicoccus Bifidobacterium Pseudomonas P.copri F.prausnitzii Oscillospira S.anginosus S.agalactiae G.elegans A.psychrolactophilus P.melaninogenica P.pallens Lachnospiraceae_uncultured_clone C.BVAB3_M_indolicus B.extructa Sneathia Rs L.jensenii L.johnsonii_gasseri_taiwanensis L.reuteri_cluster V.montpellieriensis M.hominis D.micraerophilus D.succinatiphilus_propionicifaciens Prevotella P.timonensis Leptotrichiaceae S.sanguinegens A.vaginae C.BVAB2 S.BVAB1 P.amnii Megasphaera G.vaginalis Coriobacteriaceae P.micra Gardnerella A.christensenii G.asaccharolytica. L.iners L.crispatus_acidophilus W11 SW56 W72 SW81 SW43 SW16 SW103 15 W86 10 5 0 SW78 W4 W119 W113 W125 SW67 SW87 W120 SW57 SW39 SW18 SW95 SW79 W92 W100 W88 SW84 SW53 SW70 SW24 045 W85 − SW31 68 SW54 SW104 − C.BVAB2 S.BVAB1 P.amnii Megasphaera G.vaginalis Coriobacteriaceae P.micra Gardnerella A.christensenii G.asaccharolytica. L.iners L.crispatus_acidophilus P.coxii C.hominis Porphyromonas M.curtisii Finegoldia P.corporis B.coagulans Peptostreptococcaceae Dialister C.glucuronolyticum P.niger V.cambriense Clostridium Enterobacteriaceae Staphylococcus C.tuberculostearicum F.nucleatum WAL_1855D Anaerococcus P.harei_asaccharolyticus_grossensis F.magna P.buccalis A.prevotii_tetradius P.eunonis P.lacrimalis P.bivia P.disiens M.mulieris P.anaerobius F.equinum U.parvum_urealyticum A.radingae P.harei_gorbachii P.bergensis Sutterella [Mogibacteriaceae] P.somerae Desulfovibrio M.morganii Porphyromonadaceae Clostridiales P.stomatis Moryella M.spermatophilum Campylobacter Bacteroidales S.infantis_mitis_oralis S.salivarius_thermophilus_vestibularis C.coyleae_mucifaciens C.imitans F.hominis A.octavius C.thomssenii_sundsvallense Micrococcus C.urealyticum C.tuscaniense Gallicola 1 J.anthropi Jeotgalicoccus Bifidobacterium Pseudomonas P.copri F.prausnitzii Oscillospira S.anginosus S.agalactiae G.elegans A.psychrolactophilus P.melaninogenica P.pallens Lachnospiraceae_uncultured_clone C.BVAB3_M_indolicus B.extructa Sneathia Rs L.jensenii L.johnsonii_gasseri_taiwanensis L.reuteri_cluster V.montpellieriensis M.hominis D.micraerophilus D.succinatiphilus_propionicifaciens Prevotella P.timonensis Leptotrichiaceae S.sanguinegens A.vaginae D.propionicifaciens Peptoniphilus C.ureolyticus A.hydrogenalis C.amycolatum_lactis Corynebacterium P.bennonis ph2 W112 W82 SW46 SW29 W147 SW71 SW64 SW93 SW27 W129 W11 SW62 SW72 SW56 W117 SW36 W72 SW82 SW23 SW81 W56 W51 SW43 W137 SW42 SW16 W152 SW92 SW103 SW89 SW77 W86 SW74 W33 SW78 W24 W32 W4 W65 SW48 W119 SW90 W126 W113 W95 W10 W125 W52 045 SW67 SW73 − 68 SW83 SW49 − SW87 D.propionicifaciens Peptoniphilus C.ureolyticus A.hydrogenalis C.amycolatum_lactis Corynebacterium P.bennonis ph2 P.coxii C.hominis Porphyromonas M.curtisii Finegoldia P.corporis W99B.coagulans Peptostreptococcaceae Dialister C.glucuronolyticum P.niger V.cambriense Clostridium Enterobacteriaceae Staphylococcus C.tuberculostearicum F.nucleatum WAL_1855D Anaerococcus P.harei_asaccharolyticus_grossensis F.magna P.buccalis A.prevotii_tetradius P.eunonis P.lacrimalis P.bivia P.disiens M.mulieris P.anaerobius F.equinum U.parvum_urealyticum A.radingae P.harei_gorbachii P.bergensis Sutterella [Mogibacteriaceae] P.somerae Desulfovibrio M.morganii Porphyromonadaceae Clostridiales P.stomatis Moryella M.spermatophilum Campylobacter Bacteroidales S.infantis_mitis_oralis S.salivarius_thermophilus_vestibularis C.coyleae_mucifaciens C.imitans F.hominis A.octavius C.thomssenii_sundsvallense Micrococcus C.urealyticum C.tuscaniense Gallicola 1 J.anthropi Jeotgalicoccus Bifidobacterium Pseudomonas P.copri F.prausnitzii Oscillospira S.anginosus S.agalactiae G.elegans A.psychrolactophilus P.melaninogenica P.pallens Lachnospiraceae_uncultured_clone C.BVAB3_M_indolicus B.extructa Sneathia Rs L.jensenii L.johnsonii_gasseri_taiwanensis L.reuteri_cluster V.montpellieriensis M.hominis D.micraerophilus D.succinatiphilus_propionicifaciens Prevotella P.timonensis Leptotrichiaceae S.sanguinegens A.vaginae C.BVAB2 S.BVAB1 P.amnii Megasphaera G.vaginalis Coriobacteriaceae P.micra Gardnerella A.christensenii G.asaccharolytica. L.iners L.crispatus_acidophilus W31 W120 W27 SW47 SW57 SW59 SW58 SW39 SW44 W11 W149 SW18 SW97 SW95 SW56 SW32 W72 W128 SW34 SW79 SW81 SW60 W92 SW43 SW17 SW16 W21 W100 SW80 SW103 SW88 W88 SW76 W86 SW65 SW84 SW78 W45 W4 W132 SW53 W40 W119 W7 SW70 W116 W113 W23 SW24 W125 W81 SW67 W124 W85 SW38 SW87 W43 SW31 W8 W120 W70 SW54 SW57 SW91 SW39 SW50 SW104 W89 SW18 W37 W112 W106 SW95 W130 W82 SW79 W28 W92 SW102 SW46 SW25 W100 W154 SW29 W122 W88 W74 W147 SW84 W48 SW53 W13 SW71 W77 SW70 W17 SW64 W96 SW24 W30 SW93 W85 SW55 SW31 SW26 SW27 W63 SW54 W91 W129 SW104 W136 SW101 SW62 W112 W79 W82 W68 SW72 SW68 SW46 SW28 W117 SW29 SW66 SW35 SW36 W147 SW33 SW71 W110 SW82 W54 SW64 SW94 SW23 SW93 W139 W94 W56 SW27 W131 W129 SW63 W51 SW61 SW62 W2 W137 SW72 W127 SW100 SW42 W117 SW45 SW36 SW37 W152 W6 SW82 SW75 SW92 SW23 W108 SW99 SW89 W56 W87 W51 W57 SW77 W141 W137 W35 SW74 SW42 W36 W9 W33 W152 W97 SW92 W39 W24 SW69 SW89 W84 W32 SW77 W71 W114 W65 SW74 W101 W33 W53 SW48 W15 W24 W102 euclidean / average distance | rows: SW90 W32 SW98 W73 W126 W65 SW96 W95 SW48 SW90 W10 W126 W52 W95 SW73 W10 W52 SW83 SW73 SW49 SW83 W99 SW49 W99 as input, respectively. Clustering parameters were as W31 W31 W27 W27 SW47 SW47 SW59 SW59 SW58 SW58 SW44 SW44 W149 W149 SW97 SW32 SW97 W128 SW32 SW34 W128 SW60 SW17 SW34 W21 SW60 SW80 SW17 SW88 SW76 W21 SW65 SW80 W45 SW88 W132 W40 SW76 W7 SW65 W116 -dominant subtype (C3). The biomarkers model was able to W45 W23 W81 W132 W124 W40 SW38 W7 W43 W8 W116 W70 W23 SW91 Unsupervised clustering of women according to their vaginal W81 SW50 W89 W124 W37 SW38 W106 W43 W130 W28 W8 SW102 W70 SW25 SW91 W154 W122 SW50 W74 W89 W48 W37 W13 W77 compositional subtypes were established by fuzzy clustering iners W106 W17 W130 W96 W28 W30 SW55 SW102 SW26 SW25 W63 W154 W91 W136 W122 SW101 W74 W79 W48 W68 SW68 W13 SW28 L. W77 SW66 W17 SW35 SW33 metagenome W96 W110 W30 W54 SW55 SW94 W139 SW26 W94 W63 W131 W91 SW63 SW61 W136 W2 SW101 W127 W79 SW100 SW45 W68 SW37 SW68 W6 SW28 SW75 W108 SW66 SW99 SW35 W87 SW33 W57 W141 W110 W35 W54 W36 SW94 W9 W97 W139 W39 W94 SW69 W131 W84 SW63 W71 W114 SW61 W101 W2 W53 W15 W127 euclidean / average distance | rows: W102 SW100 SW98 SW45 W73 SW37 SW96 W6 Microbiome SW75 W108 SW99 W87 W57 W141 W35 . W36 W9 W97 W39 SW69 W84 W71 W114 W101 W53 W15 W102 euclidean / average distance | rows: SW98 W73 SW96 subtype (C2), and a between C2 and C3. C1from C2and C3, but didnotdifferentiate clearly differentiate probability < 60% downstream analyses The (N=13). of three bacterial community subtypes identified included belonging to a any mixed group of with several BV-associated the bacteria (C1), three a clusters were excluded from inferred community follows: membership exponent = 1.25, dissimilarity measure = Bray-Curtis; members with Supplementary Figure 1: microbiota using the R package ‘cluster’ with k=3, using 16S microbial count data or the .
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    HATCHERIES, DEALERS, AND INDEPENDENT FLOCKS PARTICIPATING IN THE NATIONAL POULTRY IMPROVMENT PLAN MULTIPLIER EGG TYPE CHICKEN BREEDING FLOCKS HATCHING PRODUCTS CLASSIFIED ADDITIONAL NPIP. SUBPART PARTICIPANTS NAME AND ADDRESS EGG U.S. PULLORUM-TYPHOID CLASSIFICATIONS FOR NO. CAPACITY CLEAN WHICH PRODUCTS QUALFIED 43 - Missouri Clean State status Last change made on September 27, 2021 US Pullorum-Typhoid Clean State JENNIFER WEBER MR. TONY PERRYMAN POULTRY HEALTH PROGRAM MANAGER MO DEPT OF AGRICULTURE MO DEPT. OF AGRICULTURE PO BOX 630 1616 MISSOURI BLVD. JEFFERSON CITY, MO 65102 JEFFERSON CITY, MO 65102 Phone: 573-522-3378 Fax:573-751-6919 Phone: 573-526-4673 Fax:573-751-6919 [email protected] [email protected] Dealer 259 B BOLIVAR PULLETS, INC. ,1184 EAST 460TH ROAD BOLIVAR, S10B S10W S15B S25B AI CLEAN MG MS SE MO 65613 Phone: 417-326-2434 S25W S36 S42B S39 654 B MANSFIELD PULLET COMPANY, INC. ,29421 STATE HIGHWAY S36 38, MARSHFIELD, MO 65706 Phone: 417.468.5685 Independent Flocks 511 B CHARLES RIVER LABORATORIES, AVIAN PRODUCTS & SERVICE ,208 S3W MG MS SOUTH COOL SPRINGS ROAD O'FALLON, MO 63366 Page 1 of 17 HATCHERIES, DEALERS, AND INDEPENDENT FLOCKS PARTICIPATING IN THE NATIONAL POULTRY IMPROVMENT PLAN MULTIPLIER MEAT-TYPE CHICKEN BREEDING FLOCKS HATCHING PRODUCTS CLASSIFIED ADDITIONAL NPIP. SUBPART PARTICIPANTS NAME AND ADDRESS EGG U.S. PULLORUM-TYPHOID CLASSIFICATIONS FOR NO. CAPACITY CLEAN WHICH PRODUCTS QUALFIED 43 - Missouri Clean State status Last change made on September 27, 2021 US Pullorum-Typhoid Clean State JENNIFER WEBER MR. TONY PERRYMAN POULTRY HEALTH PROGRAM MANAGER MO DEPT OF AGRICULTURE MO DEPT.
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