PRJNA862629 SRP388320
Gut resistome profiling in Segamat, Malaysia community
Segamat Resistome Profiling
200 samples from a healthy community cohort in Segamat, Malaysia (adults, elderly, adolescents, children), profiling gut antibiotic resistance genes via shotgun metagenomics in a cross-sectional design. machine-written summary
200 samples · 200 runs · MY · Adult · 2023 · 7.77 Gbp / sample
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Sources
✓ Sequence archive 1,797 ✓ Abstract / description 400 ✓ Full text 200 ✓ Supplementary tables 800 – External resources– User contribution– Human verified
Checked this project's papers and archive records yourself? Mark it human-verified .
what each source gave ✓ Sequence archive1,797 sample values (age, bmi, collection date, country, latitude, location locality, location region, longitude) ✓ Abstract / description400 sample values (health condition, health condition detail) ✓ Full text200 sample values (subject id) · PMC10423249 ✓ Supplementary tables800 sample values (family id, family role, shared setting id, shared setting type) – External resourcesnot covered by the external resources we ingest – User contributionnothing uploaded yet – Human verifiednot yet checked by a person · I checked this project — verify it
Samples at a glance
1 sampling locations · 1 country
Age
adult 140
elderly 26
adolescent 21
child 13
Condition
healthy_control 200
Sequencing depth per sample ·
all projects, 0–0.03 Gbp: 25,080 samples (4 %) all projects, 0.03–0.1 Gbp: 17,066 samples (3 %) all projects, 0.1–0.3 Gbp: 29,179 samples (5 %) all projects, 0.3–1 Gbp: 47,044 samples (8 %) all projects, 1–3 Gbp: 124,983 samples (22 %) this project, 1–3 Gbp: 1 samples all projects, 3–10 Gbp: 253,728 samples (44 %) this project, 3–10 Gbp: 177 samples all projects, 10–30 Gbp: 72,533 samples (13 %) this project, 10–30 Gbp: 22 samples all projects, 30–100 Gbp: 3,024 samples (1 %) all projects, 100–300 Gbp: 106 samples (0 %) all projects, ≥ 300 Gbp: 9 samples (0 %) project median 7.77 Gbp per sample 0 1 30 Gbp
Sampling design and relatedness
community households
200 participants from 102 households in 3 Segamat localities (Bekok, Chaah, Jabi); 69 households with >=2 sampled members · 69 families with 167 sampled people · 3 shared settings.
household_member H household_member H 47 × household_member×2
household_member H household_member H household_member H 17 × household_member×3
household_member H household_member H household_member H household_member H 4 × household_member×4
household_member H household_member H household_member H household_member H household_member H household_member H 1 × household_member×6
family 10 family 10 SAMN29984887 — household member · 1 sample H 7 SAMN29984888 — household member · 1 sample H 8 SAMN2998488… family 100 family 100 SAMN29984998 — household member · 1 sample H 4998 SAMN29984999 — household member · 1 sample H 4999 SAMN29985000 — household member · 1 sample H 5000 SAMN2998… family 126 family 126 SAMN29984863 — household member · 1 sample H 3 SAMN29984864 — household member · 1 sample H 4 SAMN29984865 — household member · 1 sample H 5 SAMN29984866 — household member · 1 sample H 6 SAMN2998486… family 144 family 144 SAMN29984871 — household member · 1 sample H 871 SAMN29984875 — household member · 1 sample H 875 SAMN29984876 — household member · 1 sample H 876 SAMN29984877 — household member · 1 sample H 877 SAMN29984941 — household member · 1 sample H 941 SAMN29984943 — household member · 1 sample H 943 SAMN29984… family 104 family 104 SAMN29984839 — household member · 1 sample H 839 SAMN29984929 — household member · 1 sample H 929 SAMN29984… family 128 family 128 SAMN29984961 — household member · 1 sample H 1 SAMN29984962 — household member · 1 sample H 2 SAMN29984963 — household member · 1 sample H 3 SAMN2998496… family 155 family 155 SAMN29984970 — household member · 1 sample H 70 SAMN29984971 — household member · 1 sample H 71 SAMN29984972 — household member · 1 sample H 72 SAMN29984981 — household member · 1 sample H 81 SAMN299849… family 105 family 105 SAMN29984845 — household member · 1 sample H 4845 SAMN29985034 — household member · 1 sample H 5034 SAMN2998… family 130 family 130 SAMN29984853 — household member · 1 sample H 853 SAMN29984854 — household member · 1 sample H 854 SAMN29984930 — household member · 1 sample H 930 SAMN29984… family 47 family 47 SAMN29984964 — household member · 1 sample H 4 SAMN29984965 — household member · 1 sample H 5 SAMN29984968 — household member · 1 sample H 8 SAMN29984969 — household member · 1 sample H 9 SAMN2998496… family 108 family 108 SAMN29984840 — household member · 1 sample H 0 SAMN29984841 — household member · 1 sample H 1 SAMN2998484… family 139 family 139 SAMN29984984 — household member · 1 sample H 4 SAMN29984985 — household member · 1 sample H 5 SAMN29984988 — household member · 1 sample H 8 SAMN2998498… family 7 family 7 SAMN29984879 — household member · 1 sample H 79 SAMN29984880 — household member · 1 sample H 80 SAMN29984881 — household member · 1 sample H 81 SAMN29984882 — household member · 1 sample H 82 SAMN299848… family 112 family 112 SAMN29984844 — household member · 1 sample H 4844 SAMN29985033 — household member · 1 sample H 5033 SAMN2998… family 146 family 146 SAMN29984954 — household member · 1 sample H 4 SAMN29984955 — household member · 1 sample H 5 SAMN29984956 — household member · 1 sample H 6 SAMN2998495… family 118 family 118 SAMN29984846 — household member · 1 sample H 6 SAMN29984847 — household member · 1 sample H 7 SAMN2998484… family 151 family 151 SAMN29984946 — household member · 1 sample H 6 SAMN29984947 — household member · 1 sample H 7 SAMN29984948 — household member · 1 sample H 8 SAMN2998494… family 119 family 119 SAMN29984842 — household member · 1 sample H 2 SAMN29984843 — household member · 1 sample H 3 SAMN2998484… family 153 family 153 SAMN29985001 — household member · 1 sample H 1 SAMN29985002 — household member · 1 sample H 2 SAMN29985003 — household member · 1 sample H 3 SAMN2998500… family 12 family 12 SAMN29984884 — household member · 1 sample H 4 SAMN29984885 — household member · 1 sample H 5 SAMN2998488… family 165 family 165 SAMN29985016 — household member · 1 sample H 6 SAMN29985017 — household member · 1 sample H 7 SAMN29985018 — household member · 1 sample H 8 SAMN2998501… family 122 family 122 SAMN29984938 — household member · 1 sample H 8 SAMN29984939 — household member · 1 sample H 9 SAMN2998493… family 18 family 18 SAMN29984899 — household member · 1 sample H 899 SAMN29984902 — household member · 1 sample H 902 SAMN29984903 — household member · 1 sample H 903 SAMN29984… family 124 family 124 SAMN29984849 — household member · 1 sample H 49 SAMN29984850 — household member · 1 sample H 50 SAMN299848… village or community Bekok · 110 people village or community Bekok SAMN29984858 — member · 1 sample 58 SAMN29984859 — member · 1 sample 59 SAMN29984860 — member · 1 sample 60 SAMN29984861 — member · 1 sample 61 SAMN29984862 — member · 1 sample 62 SAMN29984863 — member · 1 sample 63 SAMN29984864 — member · 1 sample 64 SAMN29984865 — member · 1 sample 65 SAMN29984866 — member · 1 sample 66 SAMN29984867 — member · 1 sample 67 SAMN29984868 — member · 1 sample 68 SAMN29984869 — member · 1 sample 69 SAMN29984870 — member · 1 sample 70 SAMN29984871 — member · 1 sample 71 SAMN29984872 — member · 1 sample 72 SAMN29984873 — member · 1 sample 73 SAMN29984874 — member · 1 sample 74 SAMN29984875 — member · 1 sample 75 SAMN29984876 — member · 1 sample 76 SAMN29984877 — member · 1 sample 77 SAMN299848… +90 village or community Chaah · 45 people village or community Chaah SAMN29984840 — member · 1 sample 40 SAMN29984841 — member · 1 sample 41 SAMN29984842 — member · 1 sample 42 SAMN29984843 — member · 1 sample 43 SAMN29984844 — member · 1 sample 44 SAMN29984845 — member · 1 sample 45 SAMN29984846 — member · 1 sample 46 SAMN29984847 — member · 1 sample 47 SAMN29984848 — member · 1 sample 48 SAMN29984849 — member · 1 sample 49 SAMN29984850 — member · 1 sample 50 SAMN29984851 — member · 1 sample 51 SAMN29984852 — member · 1 sample 52 SAMN29984853 — member · 1 sample 53 SAMN29984854 — member · 1 sample 54 SAMN29984855 — member · 1 sample 55 SAMN29984856 — member · 1 sample 56 SAMN29984857 — member · 1 sample 57 SAMN29984879 — member · 1 sample 79 SAMN29984880 — member · 1 sample 80 SAMN299848… +25 village or community Jabi · 45 people village or community Jabi SAMN29984839 — member · 1 sample 839 SAMN29984929 — member · 1 sample 929 SAMN29984957 — member · 1 sample 957 SAMN29984958 — member · 1 sample 958 SAMN29984959 — member · 1 sample 959 SAMN29984960 — member · 1 sample 960 SAMN29984961 — member · 1 sample 961 SAMN29984962 — member · 1 sample 962 SAMN29984963 — member · 1 sample 963 SAMN29984966 — member · 1 sample 966 SAMN29984967 — member · 1 sample 967 SAMN29984970 — member · 1 sample 970 SAMN29984971 — member · 1 sample 971 SAMN29984972 — member · 1 sample 972 SAMN29984973 — member · 1 sample 973 SAMN29984974 — member · 1 sample 974 SAMN29984975 — member · 1 sample 975 SAMN29984976 — member · 1 sample 976 SAMN29984977 — member · 1 sample 977 SAMN29984978 — member · 1 sample 978 SAMN29984… +25
Families (25 of 69) How longitudinal and relatedness information is derived
Community composition
Bifidobacterium 18.5%Prevotella 8.1%Faecalibacterium 6.3%Blautia_A 6.0%Collinsella 5.7%Roseburia 3.6%Bacteroides 2.7%Gemmiger 2.4%Ruminococcoides 2.1%Phocaeicola 1.9%Holdemanella 1.5%Mediterraneibacter 1.4%
Genera, mean relative abundance over 183 profiled gut samples of this project (Sandpiper SingleM profiles, GTDB R232; low-depth and non-metagenome profiles left out).
Papers (1)
Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia. 2023 PMID 37573460 PMC10423249 own_data
Details
Archive description Profile the resistome profile based on the gut microbiota of a segamat community
How this project entered the registry Classified as human gut / stool shotgun DNA metagenome of adult and elderly and child by sonnet_x2 with confidence 0.62. Assay shotgun_dna .
host run.host_tax_id · “9606”body site study.description · “gut microbiota of a segamat community”life stage sample.attr.age · “54 (n=132/200)”life stage sample.attr.age · “69 (n=33/200)”life stage sample.attr.age · “11 (n=21/200)”Evidence examples (one per field × route)
sample field value route conf. source quote
SAMN29984839 age_at_collection_days 23010.8 R1 0.70 sample.attr.age 63 SAMN29984839 bmi 28.03 R1 0.90 sample.attr.bmi 28.0264541425497 SAMN29984839 collection_date 2018-06-29 R1 0.90 biosample.attribute:collection_date 2018-06-29 SAMN29984839 country MY R1 0.90 sample.attr.geo_loc_name Malaysia: Segamat SAMN29984839 family_id 104 R2 0.80 paper.supp.41522_2023_425_MOESM1_ESM.xlsx[suppl_tab1!household] id JD-77 household 104 SAMN29984839 family_role household_member R2 0.60 paper.supp.41522_2023_425_MOESM1_ESM.xlsx[suppl_tab1!household] 200 community participants from 102 households were recruited SAMN29984839 health_condition healthy_control R4 0.35 paper.abstract 200 individuals in Malaysia using shotgun metagenomic sequencing SAMN29984839 health_condition_detail Community-based sample; health status not explicitly stated R4 0.35 paper.abstract 200 individuals in Malaysia using shotgun metagenomic sequencing SAMN29984839 latitude 2.5035 R1 0.90 biosample.attribute:lat_lon 2.5035 N 102.8208 E SAMN29984839 location_locality Segamat R1 0.85 biosample.attribute:geo_loc_name Malaysia: Segamat SAMN29984839 location_region Johor R1 0.60 biosample.attribute:lat_lon 2.5035 N 102.8208 E SAMN29984839 longitude 102.8208 R1 0.90 biosample.attribute:lat_lon 2.5035 N 102.8208 E SAMN29984839 sex male R1 0.90 sample.attr.sex male SAMN29984839 shared_setting_id Jabi R2 0.80 paper.supp.41522_2023_425_MOESM1_ESM.xlsx[suppl_tab1!Location] id JD-77 Location Jabi SAMN29984839 shared_setting_type village_or_community R2 0.80 paper.supp.41522_2023_425_MOESM1_ESM.xlsx[suppl_tab1!Location] id JD-77 Location Jabi SAMN29984839 subject_id SAMN29984839 R3 0.70 design.one_sample_per_subject:fulltext A total of 200 community participants from 102 households were recruited from the South East Asia Community Observatory
Sequencing 200 runs over 200 samples · mean 7.91 Gbp per run (median 7.77 Gbp, total 1,582.92 Gbp; 200 runs with a base count) · layout PAIRED 200 · platform ILLUMINA 200 · models Illumina MiSeq (200) · 92% of runs with a Sandpiper profile · first public 2023-08-01
Authors (9) Dwiyanto J first · Huët MAL · Hussain MH · Su TT · Tan JBL · Toh KY · Lee JWJ · Rahman S · Chong CW last
Downloads PRJNA862629.csv.gz (8.6 KB) · parquet (83.4 KB) — all 200 samples, every field with route and confidence · PRJNA862629_determinations.csv.gz (29.5 KB) — 3,197 evidence rows
Samples (200 · every field this project has values for · hover a cell for its source)
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