ampliconflow
Archive records ENA PRJNA796316 SRA PRJNA796316 BioProject PRJNA796316

opens the authoritative record at ENA, SRA or BioSample; this page never replaces it

PRJNA796316 released 25 Sept 2026

PRJNA796316

Pipeline 0.1.0 Contract v0.1 Licence CC-BY-4.0

Tags

derived from the release metadata, not hand-written

Study

The study record carries no description, and its registered title is the accession itself. The figures below are computed from the 11 released samples and 11 runs.

Samples
11
Runs
11
Collection
2016-05 to 2016-05

Linked publication

No publication linked for this study.

Location

sampling sites from the release coordinates

No sample coordinates in this release

The study reports no latitude or longitude, and its metadata carries no lat_lon text field either, so no map or place-name hierarchy can be drawn. Every other panel is computed from the count table and the sample metadata.

How the sequences were obtained

sample to release
01 study metadata

Sample collection

11 samples, 2016-05 to 2016-05

no coordinates in the release

02 not reported

Storage

not reported

neither the archive nor the linked paper states storage conditions

03 not reported

Processing

not reported

no extraction kit or lysis protocol in the archive or the linked paper

04 per-run QC

PCR

16S rRNA V4-V5

primers: trimmed; polymerase, cycle count and primer sequences are not stated in the linked paper

05 not reported

Sequencing preparation

not reported

no library kit or index strategy in the archive or the linked paper

06 study metadata

Sequencing

Illumina MiSeq

11 runs; PAIRED 251.0 bp reads

07 this release

Denoising

dada2 1.38.0

1,033 ASVs from 665,257 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 665,257 reads from 11 runs, QC to 98.2% 16S identity and 92.1% above Q30, primers trimmed, dada2 1.38.0 to 1,033 ASVs, taxonomy against a SINTAX reference, then the release (CC-BY-4.0).

Steps 1 to 6 are how the sequences were obtained, from the study's own archive metadata. Step 7 is what the authors report doing with the sequences in the linked paper. ampliconflow starts at the deposited reads rather than repeating the wet lab.

Taxonomy assigned with SILVA 138.2 (SINTAX).

11

Samples

11 runs

1k

Features

OTUs at 97%

665.3k

Reads

mapped total

136 MB

Release size

54 files

Depth floor

1,000 reads

no samples below

Reads per sample

log scale
min
36,779
median
63,119
max
87,738

Feature detection

100.0% non-zero

1,033 / 1,033 features

Features with at least one observed read. The remainder are present in the reference set but not detected in these samples.

Composition

Top phyla

  • Pseudomonadota 286,588 (43.1%)
  • Campylobacterota 99,222 (14.9%)
  • Bacillota 84,817 (12.7%)
  • Bacteroidota 55,509 (8.3%)
  • Deinococcota 36,034 (5.4%)
  • Actinomycetota 34,420 (5.2%)
  • Thermodesulfobacteriota 26,372 (4.0%)
  • Rhodothermota 11,186 (1.7%)
  • Nitrospirota 4,623 (0.7%)
  • Chloroflexota 4,098 (0.6%)
  • Myxococcota 2,990 (0.4%)
  • Cyanobacteriota 2,843 (0.4%)
  • Spirochaetota 2,833 (0.4%)
  • Verrucomicrobiota 2,600 (0.4%)
  • Schekmanbacteria 1,761 (0.3%)
  • Sva0485 1,525 (0.2%)
  • Patescibacteria 1,376 (0.2%)
  • Planctomycetota 1,009 (0.2%)
  • Acidobacteriota 928 (0.1%)
  • Candidatus Kapabacteria 876 (0.1%)

Top genera

  • Aeromonas 133,585 (20.1%)
  • Enterobacter 54,163 (8.1%)
  • Bacteroides 47,729 (7.2%)
  • Incertae Sedis 45,857 (6.9%)
  • Sulfurovum 45,193 (6.8%)
  • Sulfurimonas 44,995 (6.8%)
  • Thermus 35,044 (5.3%)
  • Bifidobacterium 32,996 (5.0%)
  • Acinetobacter 16,750 (2.5%)
  • Humidesulfovibrio 12,861 (1.9%)
  • Streptococcus 11,836 (1.8%)
  • Rhodothermus 11,186 (1.7%)
  • Pseudomonas 9,578 (1.4%)
  • Exiguobacterium 8,797 (1.3%)
  • Enterococcus 7,291 (1.1%)
  • Staphylococcus 6,317 (0.9%)
  • Thiothrix 5,487 (0.8%)
  • Thermodesulfitimonas 5,111 (0.8%)
  • Rugosibacter 5,008 (0.8%)
  • Thiomicrorhabdus 4,861 (0.7%)

Rank-abundance

log-log
1 10 100 1k 1 10 100 ASV_1 · Bacteroides: 8188 reads ASV_2 · Aeromonas: 7377 reads ASV_3 · Aeromonas: 5309 reads ASV_4 · Sulfurovum: 5096 reads ASV_5 · Bacteroides: 4872 reads ASV_6 · Aeromonas: 4824 reads ASV_7 · Enterobacter: 4627 reads ASV_8 · Sulfurimonas: 4332 reads ASV_9 · Enterobacter: 4215 reads ASV_10 · Bifidobacterium: 4118 reads ASV_11 · Sulfurovum: 4114 reads ASV_12 · Enterobacter: 4089 reads ASV_13 · Bacteroides: 4066 reads ASV_14 · Enterobacter: 4053 reads ASV_15 · Arcobacter: 3952 reads ASV_16 · Enterobacter: 3899 reads ASV_17 · Humidesulfovibrio: 3866 reads ASV_18 · Bacteroides: 3740 reads ASV_19 · Desulfocapsa: 3732 reads ASV_20 · Thermus: 3692 reads ASV_21 · Staphylococcus: 3616 reads ASV_22 · Aeromonas: 3287 reads ASV_23 · Bacteroides: 3264 reads ASV_24 · Bacteroides: 3223 reads ASV_25 · Bifidobacterium: 3190 reads ASV_26 · Aeromonas: 3139 reads ASV_27 · Sulfurovum: 3107 reads ASV_28 · Thiomicrorhabdus: 3065 reads ASV_29 · Aeromonas: 2990 reads ASV_30 · Aeromonas: 2964 reads ASV_31 · Humidesulfovibrio: 2955 reads ASV_32 · Bacteroides: 2921 reads ASV_33 · Aeromonas: 2909 reads ASV_34 · Sulfurimonas: 2852 reads ASV_35 · Aeromonas: 2849 reads ASV_36 · Thermus: 2800 reads ASV_37 · Rugosibacter: 2775 reads ASV_38 · Incertae Sedis: 2716 reads ASV_39 · Sulfurimonas: 2714 reads ASV_40 · Sulfurimonas: 2622 reads ASV_41 · Aeromonas: 2586 reads ASV_42 · Sulfurovum: 2578 reads ASV_43 · Aeromonas: 2557 reads ASV_44 · Thioreductor: 2539 reads ASV_45 · Aeromonas: 2519 reads ASV_46 · Aeromonas: 2486 reads ASV_47 · Acinetobacter: 2483 reads ASV_48 · Thermodesulfitimonas: 2443 reads ASV_49 · Sulfurovum: 2365 reads ASV_50 · Bacteroides: 2360 reads ASV_51 · Bifidobacterium: 2349 reads ASV_52 · Clostridium: 2344 reads ASV_53 · Enterobacter: 2337 reads ASV_54 · Rhizobium: 2317 reads ASV_55 · Sulfurovum: 2299 reads ASV_56 · Bifidobacterium: 2276 reads ASV_57 · Aeromonas: 2259 reads ASV_58 · Aeromonas: 2251 reads ASV_59 · Rugosibacter: 2233 reads ASV_60 · Enterobacter: 2191 reads ASV_61 · Humidesulfovibrio: 2178 reads ASV_62 · Sulfurimonas: 2173 reads ASV_63 · Desulfocucumis: 2109 reads ASV_64 · Sulfurimonas: 2107 reads ASV_65 · Incertae Sedis: 2098 reads ASV_66 · SCADC1-2-3: 2077 reads ASV_67 · Bifidobacterium: 2064 reads ASV_68 · Enterobacter: 2049 reads ASV_69 · Rhodothermus: 2006 reads ASV_70 · Aeromonas: 2000 reads ASV_71 · Bifidobacterium: 1997 reads ASV_72 · Thermus: 1995 reads ASV_73 · Halothiobacillus: 1993 reads ASV_74 · Exiguobacterium: 1989 reads ASV_75 · Aeromonas: 1981 reads ASV_76 · Mediterraneibacter: 1979 reads ASV_77 · Aeromonas: 1948 reads ASV_78 · Streptococcus: 1929 reads ASV_79 · Aeromonas: 1927 reads ASV_80 · Bacteroides: 1900 reads ASV_81 · Aeromonas: 1872 reads ASV_82 · Acidithiobacillus: 1860 reads ASV_83 · Neisseria: 1855 reads ASV_84 · Aeromonas: 1842 reads ASV_85 · Aeromonas: 1830 reads ASV_86 · Aeromonas: 1824 reads ASV_87 · Bacteroides: 1804 reads ASV_88 · Sulfurimonas: 1800 reads ASV_89 · Sulfurovum: 1798 reads ASV_90 · Desulfurivibrio: 1791 reads ASV_91 · Sulfurovum: 1780 reads ASV_92 · Sulfurimonas: 1767 reads ASV_93 · Thermus: 1742 reads ASV_94 · Acinetobacter: 1741 reads ASV_95 · Aeromonas: 1729 reads ASV_96 · Erysipelotrichaceae UCG-003: 1706 reads ASV_97 · Aeromonas: 1685 reads ASV_98 · Incertae Sedis: 1678 reads ASV_99 · Aeromonas: 1669 reads ASV_100 · Aeromonas: 1652 reads ASV_101 · Aeromonas: 1644 reads ASV_102 · Thiovirga: 1644 reads ASV_103 · Aeromonas: 1639 reads ASV_104 · Bifidobacterium: 1628 reads ASV_105 · Acinetobacter: 1605 reads ASV_106 · Bifidobacterium: 1603 reads ASV_107 · Incertae Sedis: 1599 reads ASV_108 · Acinetobacter: 1591 reads ASV_109 · Enterobacter: 1582 reads ASV_110 · Aeromonas: 1561 reads ASV_111 · Bacillus: 1553 reads ASV_112 · Pseudomonas: 1535 reads ASV_113 · Rhodothermus: 1523 reads ASV_114 · Aeromonas: 1517 reads ASV_115 · Bifidobacterium: 1512 reads ASV_116 · Thermus: 1503 reads ASV_117 · Thermus: 1496 reads ASV_118 · Aeromonas: 1475 reads ASV_119 · Humidesulfovibrio: 1462 reads ASV_120 · Hydrogenovibrio: 1460 reads ASV_121 · Aeromonas: 1450 reads ASV_122 · Sulfurimonas: 1448 reads ASV_123 · Enterococcus: 1444 reads ASV_124 · Aeromonas: 1443 reads ASV_125 · Geitlerinema PCC-8501: 1422 reads ASV_126 · Humidesulfovibrio: 1421 reads ASV_127 · Rhodothermus: 1414 reads ASV_128 · Streptococcus: 1410 reads ASV_129 · Thiothrix: 1409 reads ASV_130 · Bifidobacterium: 1402 reads ASV_131 · Aeromonas: 1402 reads ASV_132 · Enterobacter: 1401 reads ASV_133 · Turneriella: 1397 reads ASV_134 · Aeromonas: 1391 reads ASV_135 · Acinetobacter: 1390 reads ASV_136 · Sulfurovum: 1387 reads ASV_137 · Bifidobacterium: 1384 reads ASV_138 · Streptococcus: 1380 reads ASV_139 · Thiothrix: 1363 reads ASV_140 · Enterobacter: 1349 reads ASV_141 · Aeromonas: 1349 reads ASV_142 · Sulfurovum: 1348 reads ASV_143 · Latilactobacillus: 1346 reads ASV_144 · Pseudomonas: 1336 reads ASV_145 · Lactobacillus: 1335 reads ASV_146 · Incertae Sedis: 1324 reads ASV_147 · Aeromonas: 1323 reads ASV_148 · Incertae Sedis: 1313 reads ASV_149 · Incertae Sedis: 1306 reads ASV_150 · Sulfurovum: 1300 reads ASV_151 · Thermus: 1293 reads ASV_152 · Pseudomonas: 1288 reads ASV_153 · Incertae Sedis: 1286 reads ASV_154 · Exiguobacterium: 1285 reads ASV_155 · Blautia: 1275 reads ASV_156 · Incertae Sedis: 1273 reads ASV_157 · Thermus: 1273 reads ASV_158 · Aeromonas: 1272 reads ASV_159 · Streptococcus: 1267 reads ASV_160 · Acinetobacter: 1263 reads ASV_161 · Thiomicrorhabdus: 1257 reads ASV_162 · Rhodothermus: 1257 reads ASV_163 · Leuconostoc: 1245 reads ASV_164 · Bifidobacterium: 1240 reads ASV_165 · Thermus: 1240 reads ASV_166 · Sulfurovum: 1238 reads ASV_167 · Enterococcus: 1235 reads ASV_168 · Aeromonas: 1228 reads ASV_169 · Aeromonas: 1226 reads ASV_170 · Sulfurovum: 1224 reads ASV_171 · Aeromonas: 1220 reads ASV_172 · Thiomicrospira: 1218 reads ASV_173 · Bacteroides: 1218 reads ASV_174 · Erythrobacter: 1214 reads ASV_175 · Acinetobacter: 1213 reads ASV_176 · Pseudomonas: 1209 reads ASV_177 · Streptococcus: 1205 reads ASV_178 · Bifidobacterium: 1204 reads ASV_179 · Acidihalobacter: 1173 reads ASV_180 · Pseudomonas: 1172 reads ASV_181 · Pseudoclostridium: 1168 reads ASV_182 · Sulfurimonas: 1162 reads ASV_183 · Streptococcus: 1161 reads ASV_184 · Sulfurovum: 1159 reads ASV_185 · Bifidobacterium: 1159 reads ASV_186 · Agrobacterium: 1158 reads ASV_187 · Aeromonas: 1157 reads ASV_188 · Streptococcus: 1155 reads ASV_189 · Thiovirga: 1154 reads ASV_190 · Bacteroides: 1143 reads ASV_191 · Incertae Sedis: 1134 reads ASV_192 · Aeromonas: 1121 reads ASV_193 · Hydrogenophilus: 1115 reads ASV_194 · Listeria: 1115 reads ASV_195 · Thermus: 1112 reads ASV_196 · Aeromonas: 1111 reads ASV_197 · Bifidobacterium: 1095 reads ASV_198 · Aeromonas: 1089 reads ASV_199 · Sulfurovum: 1089 reads ASV_200 · Aeromonas: 1084 reads rank reads

1,033 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

11 samples
min
36,779
median
63,119
max
87,738

Downstream QC and analysis

computed from the released tables

Eleven modules, computed from the released count table, the sample metadata and the per-run QC reports. Each panel states its own n and the test it used; a module that cannot run on this release is shown as a flagged gap rather than an empty frame.

Rarefaction

median with p10 to p90
2k 5k 10k 20k 50k 151 0

Expected richness when 11 samples are subsampled to a common depth, resampled 31 draws. Median 82 features observed at full depth.

Depth against richness

log depth
161 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.541, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 98.2% alignment call per run
  • Q30 rate 92.1% mean Q 35.9
  • Amplicon V4-V5 primers trimmed
  • PhiX 0.0% control spike-in

11 run report(s), n/a GC, 0.0% ambiguous bases.

Diversity

Shannon
3.86
Simpson
0.971
Evenness
0.875
Chao1
82

Median across samples. Observed richness ranges 30 to 161.

Feature prevalence

0 of 1,033 features

present in at least half of the 11 samples (0.0%). 1,033 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 11 plotted. Choose the axes and the colour variable; hover a point for its sample id. The legend below the axes names the levels or the numeric range.

What explains each axis

pc1 · 10.0%

  • observed 11.8%
  • chao1 11.8%
  • evenness 7.6%
  • shannon 6.9%

pc2 · 10.0%

  • pH 26.1%
  • observed 11.5%
  • chao1 11.5%
  • shannon 8.4%

pc3 · 10.0%

  • shannon 58.8%
  • observed 33.1%
  • chao1 33.1%
  • evenness 26.2%

Categorical variables use eta-squared (between-group share of the axis), numeric ones the squared Pearson correlation. Computed from the released sample metadata.

Alpha diversity per sample

Shannon
4.4 11 samples

Median Shannon 3.860 across the release; observed richness runs 30 to 161.

Bray-Curtis dissimilarity

11 x 11, darker is closer

Sample order is the release order, 11 labels, and the matrix itself ships as beta_distance.tsv beside the analysis.

Phylogenetic diversity

Not available for this release: no Newick tree beside the table; run the tree stage, then re-run analyze. The legacy analysis computed Faith's PD when the container carried a tree, and this one reports the absence instead of an empty column.

Community states

CLR, k by silhouette

k = 3 silhouette 0.133

  • state 0 9 samples
  • state 1 1 samples
  • state 2 1 samples

Clustered on the centred log-ratio of the top 200 features; 11 samples.

Batch-bias audit

states against

adjusted Rand n/a p = n/a

not enough levels to test

permutations. Every sample here carries both MiSeq and MiniSeq runs, so the batch variable used is the one with two levels, here .

Variance partitioning

mean R2 per feature, CLR
  • pH 0.088

Joint R2 0.088, so the metadata explains a modest slice of the feature variation, and the two variables are not independent of one another.

Effect size

No two-level comparison available.

Taxa against all samples

with

features tested, 0 survive the correction at q ≤ 0.05

Nothing survives. The smallest q is n/a, which is the honest answer for a study whose samples are spread across three years with two to thirteen samples per year.

Group difference and spread

Bray-Curtis, 999 permutations
PERMANOVA pseudo-F
n/a · p n/a
PERMDISP F
n/a · p n/a
Distance decay (Mantel r)
n/a · p n/a

    The contamination class separates the communities beyond the spread within each class (PERMANOVA) with no evidence that the spread itself differs (PERMDISP). Distance decay runs over n/a to n/a km.

    Spatial structure

    observed richness over distance

    the study's coordinates fall on a single site (no spread), so spatial autocorrelation is not defined

    Constrained ordination

    contamination class as the constraint

    RDA · R2 0.100p 0.480

    Hellinger-scaled, 1 dummy predictors over 11 samples. The constraint explains 10.0% of the community inertia, 0.000 adjusted.

    CCA · p 0.825

    Chi-square weighted SVD. Not significant here, which is the honest reading at this sample size and predictor count.

    Co-occurrence network

    100 nodes · 467 edges

    positive
    467
    negative
    0
    density
    0.094
    components
    11
    mean degree
    9.3

    Spearman on log1p proportions, 100 features, |r| ≥ 0.50, FDR 0.05.

    Hubs by degree

      Phylogenetic and signal analyses need a tree

      no Newick tree beside the table; run the tree stage, then re-run analyze. The tree stage aligns the ASVs with MAFFT and builds with FastTree, both detected as external tools; neither is installed on the machine this page was built on, so Faith's PD, UniFrac, Pagel's lambda and Blomberg's K are left flagged rather than guessed.

      ASV phylogeny

      0 most abundant of the tree

      No tree in this release.

      ASV panel

      no sequence file

      The representative sequences are not in this release, so length and GC cannot be drawn.

      Most abundant ASVs

      ASVphylumgenusmeanprev.
      ASV_1BacteroidotaBacteroides744.49%
      ASV_2PseudomonadotaAeromonas670.69%
      ASV_3PseudomonadotaAeromonas482.69%
      ASV_4CampylobacterotaSulfurovum463.39%
      ASV_5BacteroidotaBacteroides442.99%
      ASV_6PseudomonadotaAeromonas438.69%
      ASV_7PseudomonadotaEnterobacter420.69%
      ASV_8CampylobacterotaSulfurimonas393.89%
      ASV_9PseudomonadotaEnterobacter383.29%
      ASV_10ActinomycetotaBifidobacterium374.49%
      ASV_11CampylobacterotaSulfurovum374.09%
      ASV_12PseudomonadotaEnterobacter371.79%

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      Missing or wrong data?

      Report a field that is empty or mistaken, or associate a paper with this study. No account is needed; the contact email is optional and used only to reply about this submission.

      Contribute to PRJNA796316

      Validated automatically where it can be, reviewed by a person where it cannot.

      Downloads

      8 files · sha256 in manifest

      Files are served from https://huggingface.co/datasets/hmacgregor/ampliconflow-releases/resolve/main/PRJNA796316-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      11 samples
      Sample Collected group Reads Features Shannon State
      SAMN24847862 2016-05-23 63,534 82 3.857 0
      SAMN24847863 2016-05-24 72,241 116 3.86 0
      SAMN24847864 2016-05-18 36,779 79 3.956 0
      SAMN24847865 2016-05-22 73,430 67 3.706 2
      SAMN24847866 2016-05-24 41,394 70 3.835 0
      SAMN24847867 2016-05-20 63,119 161 4.431 0
      SAMN24847868 2016-05-28 50,531 30 2.923 0
      SAMN24847869 2016-05-18 47,753 111 4.247 0
      SAMN24847870 2016-05-24 45,183 51 3.444 0
      SAMN24847871 2016-05-28 83,555 145 4.23 0
      SAMN24847872 2016-05-29 87,738 121 4.192 1

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