ampliconflow
Archive records ENA PRJNA254742 SRA PRJNA254742 BioProject PRJNA254742

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

PRJNA254742 released 25 Sept 2026

PRJNA254742

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 19 released samples and 33 runs.

Samples
19
Runs
33
Collection
2012 to 2012

Linked publication

No publication linked for this study.

Location

sampling sites from the release coordinates
19sampling sites · drag to pan, scroll or pinch to zoom

Place name hierarchy

  1. ▸ United States
  2. › Ohio
  3. › Franklin County

Districts named on the samples

  • Franklin County 1

Latitude 40 to 40, longitude -83.04 to -83.04. Names resolved with OpenStreetMap Nominatim from the release's own coordinates; Coordinates parsed from the released lat_lon text field, which the pipeline keeps but does not split into latitude/longitude columns.

How the sequences were obtained

sample to release
01 study metadata

Sample collection

19 samples, 2012 to 2012

40.0000 to 40.0000 N, -83.0400 to -83.0400 E

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

primers: present; 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

454 GS FLX+

33 runs; SINGLE 294.5789 bp reads

07 this release

Denoising

dada2 1.38.0

7,412 ASVs from 179,362 reads

ampliconflow branches off at step 6, Sequencing

this release

ampliconflow starts here: 179,362 reads from 33 runs, QC to 84.8% 16S identity and 89.4% above Q30, primers trimmed, dada2 1.38.0 to 7,412 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).

19

Samples

33 runs

7.4k

Features

OTUs at 97%

179.4k

Reads

mapped total

12 MB

Release size

96 files

Depth floor

1,000 reads

no samples below

QC warnings

1

3% of runs warned

Reads per sample

log scale
min
3,878
median
7,989
max
31,470

Feature detection

100.0% non-zero

7,412 / 7,412 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 75,012 (41.8%)
  • Bacillota 19,410 (10.8%)
  • Bacteroidota 15,582 (8.7%)
  • Acidobacteriota 10,590 (5.9%)
  • Verrucomicrobiota 9,761 (5.4%)
  • Actinomycetota 8,908 (5.0%)
  • Thermodesulfobacteriota 5,775 (3.2%)
  • Myxococcota 4,817 (2.7%)
  • Thermoproteota 4,206 (2.3%)
  • Chloroflexota 4,111 (2.3%)
  • Planctomycetota 3,836 (2.1%)
  • Gemmatimonadota 3,288 (1.8%)
  • Cyanobacteriota 2,494 (1.4%)
  • Nitrospirota 2,282 (1.3%)
  • Methylomirabilota 1,593 (0.9%)
  • Halobacteriota 1,125 (0.6%)
  • Bdellovibrionota 793 (0.4%)
  • Latescibacterota 548 (0.3%)
  • Armatimonadota 495 (0.3%)
  • Chlamydiota 380 (0.2%)

Top genera

  • Incertae Sedis 64,759 (36.1%)
  • Pseudomonas 18,936 (10.6%)
  • Cellvibrio 6,692 (3.7%)
  • Clostridium 3,868 (2.2%)
  • Candidatus Udaeobacter 3,695 (2.1%)
  • Massilia 3,591 (2.0%)
  • Sphingomonas 3,200 (1.8%)
  • Dechloromonas 2,486 (1.4%)
  • Geomonas 2,412 (1.3%)
  • Gracilibacter 2,410 (1.3%)
  • Phenylobacterium 2,267 (1.3%)
  • Nitrospira 2,245 (1.3%)
  • Acinetobacter 2,213 (1.2%)
  • Pseudazoarcus 2,178 (1.2%)
  • Azospirillum 2,032 (1.1%)
  • Cupriavidus 1,604 (0.9%)
  • Caulobacter 1,533 (0.9%)
  • Ruminiclostridium 1,465 (0.8%)
  • Sphingobacterium 1,412 (0.8%)
  • Oleiharenicola 1,208 (0.7%)

Rank-abundance

log-log
1 10 100 1k 1 10 100 ASV_1: 3366 reads ASV_2 · Clostridium: 1647 reads ASV_3 · Clostridium: 1263 reads ASV_4 · Cellvibrio: 1035 reads ASV_5 · Pseudomonas: 1031 reads ASV_6 · Pseudomonas: 1027 reads ASV_7 · Pseudomonas: 956 reads ASV_8 · Cellvibrio: 919 reads ASV_9 · Cellvibrio: 863 reads ASV_10 · Cellvibrio: 857 reads ASV_11 · Pseudomonas: 812 reads ASV_12 · Pseudomonas: 724 reads ASV_13 · Pseudomonas: 708 reads ASV_14 · Pseudomonas: 701 reads ASV_15 · Cellvibrio: 653 reads ASV_16 · Pseudomonas: 648 reads ASV_17 · Cellvibrio: 630 reads ASV_18 · Incertae Sedis: 628 reads ASV_19 · Incertae Sedis: 577 reads ASV_20 · Pseudomonas: 573 reads ASV_21 · Cellvibrio: 540 reads ASV_22 · Pseudomonas: 530 reads ASV_23 · Pseudomonas: 530 reads ASV_24 · Cellvibrio: 527 reads ASV_25 · Pseudomonas: 518 reads ASV_26 · Incertae Sedis: 504 reads ASV_27 · Pseudazoarcus: 491 reads ASV_28 · Pseudomonas: 458 reads ASV_29 · Incertae Sedis: 455 reads ASV_30 · Gracilibacter: 453 reads ASV_31 · Methanosarcina: 449 reads ASV_32 · Pseudomonas: 448 reads ASV_33 · Incertae Sedis: 432 reads ASV_34 · Pseudomonas: 421 reads ASV_35 · Acinetobacter: 417 reads ASV_36 · Pseudomonas: 416 reads ASV_37 · Incertae Sedis: 401 reads ASV_38 · Ruminiclostridium: 400 reads ASV_39 · Incertae Sedis: 397 reads ASV_40 · Caulobacter: 396 reads ASV_41 · Incertae Sedis: 392 reads ASV_42 · Pseudomonas: 387 reads ASV_43 · Incertae Sedis: 385 reads ASV_44 · Pseudomonas: 384 reads ASV_45 · Ruminiclostridium: 378 reads ASV_46 · Gracilibacter: 373 reads ASV_47 · Pseudomonas: 370 reads ASV_48 · Incertae Sedis: 365 reads ASV_49 · Pseudomonas: 362 reads ASV_50 · Acinetobacter: 359 reads ASV_51 · Incertae Sedis: 356 reads ASV_52 · Caulobacter: 331 reads ASV_53 · Incertae Sedis: 320 reads ASV_54 · Methanosarcina: 312 reads ASV_55 · Pseudomonas: 304 reads ASV_56 · Gracilibacter: 299 reads ASV_57 · Phenylobacterium: 293 reads ASV_58 · Acinetobacter: 290 reads ASV_59 · Acinetobacter: 284 reads ASV_60 · Incertae Sedis: 281 reads ASV_61 · Incertae Sedis: 278 reads ASV_62 · Incertae Sedis: 277 reads ASV_63 · Caulobacter: 275 reads ASV_64 · Pseudomonas: 273 reads ASV_65 · Incertae Sedis: 268 reads ASV_66 · Phenylobacterium: 258 reads ASV_67 · Pseudomonas: 258 reads ASV_68 · Pseudomonas: 257 reads ASV_69 · Incertae Sedis: 254 reads ASV_70 · Incertae Sedis: 251 reads ASV_71 · Magnetospirillum: 241 reads ASV_72 · Sphingobacterium: 240 reads ASV_73 · Pseudomonas: 240 reads ASV_74 · Sphingobacterium: 238 reads ASV_75 · Pseudomonas: 238 reads ASV_76 · Incertae Sedis: 236 reads ASV_77 · Candidatus Udaeobacter: 234 reads ASV_78 · Incertae Sedis: 234 reads ASV_79 · Cellvibrio: 225 reads ASV_80 · Incertae Sedis: 223 reads ASV_81 · Pseudomonas: 223 reads ASV_82 · Pseudomonas: 220 reads ASV_83 · Pseudomonas: 220 reads ASV_84 · Incertae Sedis: 219 reads ASV_85 · Dechloromonas: 217 reads ASV_86 · Candidatus Udaeobacter: 214 reads ASV_87 · Incertae Sedis: 213 reads ASV_88 · Incertae Sedis: 211 reads ASV_89 · Candidatus Udaeobacter: 205 reads ASV_90 · Sphingobacterium: 205 reads ASV_91 · Caulobacter: 200 reads ASV_92 · Achromobacter: 199 reads ASV_93 · Dechloromonas: 199 reads ASV_94 · Massilia: 196 reads ASV_95 · Incertae Sedis: 196 reads ASV_96 · Methyloversatilis: 195 reads ASV_97 · Noviherbaspirillum: 190 reads ASV_98 · Incertae Sedis: 190 reads ASV_99 · Incertae Sedis: 188 reads ASV_100 · Incertae Sedis: 184 reads ASV_101 · Geomonas: 183 reads ASV_102 · Massilia: 179 reads ASV_103 · Incertae Sedis: 176 reads ASV_104 · Ferrovibrio: 175 reads ASV_105 · Candidatus Udaeobacter: 175 reads ASV_106 · Incertae Sedis: 175 reads ASV_107 · Pseudomonas: 175 reads ASV_108 · Cupriavidus: 174 reads ASV_109 · Pseudomonas: 174 reads ASV_110 · Incertae Sedis: 174 reads ASV_111 · Incertae Sedis: 174 reads ASV_112 · Pseudomonas: 173 reads ASV_113 · Incertae Sedis: 172 reads ASV_114 · Azospirillum: 171 reads ASV_115 · Incertae Sedis: 171 reads ASV_116 · Sphingobacterium: 170 reads ASV_117 · Candidatus Udaeobacter: 169 reads ASV_118 · Dechloromonas: 168 reads ASV_119 · Massilia: 167 reads ASV_120 · Incertae Sedis: 167 reads ASV_121 · Incertae Sedis: 165 reads ASV_122 · Incertae Sedis: 164 reads ASV_123 · Massilia: 164 reads ASV_124 · Incertae Sedis: 163 reads ASV_125 · Incertae Sedis: 163 reads ASV_126 · Pseudomonas: 161 reads ASV_127 · Pseudazoarcus: 161 reads ASV_128 · Incertae Sedis: 159 reads ASV_129 · Cupriavidus: 159 reads ASV_130 · Sphingomonas: 158 reads ASV_131 · Incertae Sedis: 158 reads ASV_132 · Incertae Sedis: 157 reads ASV_133 · Geomonas: 157 reads ASV_134 · Magnetospirillum: 156 reads ASV_135 · Massilia: 155 reads ASV_136 · Achromobacter: 155 reads ASV_137 · Gracilibacter: 154 reads ASV_138 · Geomonas: 154 reads ASV_139 · Geomonas: 153 reads ASV_140 · Sphingobacterium: 153 reads ASV_141 · Incertae Sedis: 152 reads ASV_142 · Dyadobacter: 152 reads ASV_143 · Cupriavidus: 151 reads ASV_144 · Anaerocolumna: 151 reads ASV_145 · Exiguobacterium: 150 reads ASV_146 · Incertae Sedis: 149 reads ASV_147 · Incertae Sedis: 149 reads ASV_148 · Azospirillum: 149 reads ASV_149 · Paenibacillus: 149 reads ASV_150 · Ruminiclostridium: 148 reads ASV_151 · Massilia: 148 reads ASV_152 · Incertae Sedis: 146 reads ASV_153 · Methanosarcina: 146 reads ASV_154 · Massilia: 144 reads ASV_155 · Geomonas: 144 reads ASV_156 · Achromobacter: 144 reads ASV_157 · Massilia: 143 reads ASV_158 · Incertae Sedis: 142 reads ASV_159 · Candidatus Koribacter: 142 reads ASV_160 · Aquabacterium: 142 reads ASV_161 · Azospirillum: 142 reads ASV_162 · Sphingomonas: 141 reads ASV_163 · Gracilibacter: 140 reads ASV_164 · Ferrovibrio: 139 reads ASV_165 · Geomonas: 139 reads ASV_166 · Sphingobacterium: 139 reads ASV_167 · Dyadobacter: 138 reads ASV_168 · Phenylobacterium: 138 reads ASV_169 · Massilia: 137 reads ASV_170 · Paenibacillus: 137 reads ASV_171 · Flavobacterium: 137 reads ASV_172 · Aquabacterium: 137 reads ASV_173 · Pseudomonas: 136 reads ASV_174 · Incertae Sedis: 136 reads ASV_175 · Incertae Sedis: 135 reads ASV_176 · Incertae Sedis: 135 reads ASV_177 · Massilia: 135 reads ASV_178 · Massilia: 135 reads ASV_179 · Incertae Sedis: 135 reads ASV_180 · Sphingobacterium: 134 reads ASV_181 · Pseudomonas: 134 reads ASV_182 · Massilia: 134 reads ASV_183 · Incertae Sedis: 133 reads ASV_184 · Incertae Sedis: 133 reads ASV_185 · Dechloromonas: 133 reads ASV_186 · Thermincola: 132 reads ASV_187 · Pseudomonas: 132 reads ASV_188 · Incertae Sedis: 131 reads ASV_189 · Acinetobacter: 131 reads ASV_190 · Incertae Sedis: 130 reads ASV_191 · Massilia: 130 reads ASV_192 · Nitrospira: 129 reads ASV_193 · Incertae Sedis: 129 reads ASV_194 · Acidovorax: 129 reads ASV_195 · Geomonas: 128 reads ASV_196 · Incertae Sedis: 127 reads ASV_197 · P3OB-42: 127 reads ASV_198 · Azospirillum: 127 reads ASV_199 · Agrobacterium: 126 reads ASV_200 · Dechloromonas: 126 reads rank reads

7,412 ranked features, top 200 shown. A steep drop means a few taxa carry most of the reads.

Per-sample reads

19 samples
min
3,878
median
7,989
max
31,470

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 1,107 0

Expected richness when 19 samples are subsampled to a common depth, resampled 31 draws. Median 361 features observed at full depth.

Depth against richness

log depth
1,152 0 reads per sample, log scale

One point per sample. Correlation of log reads with observed features is 0.637, so the depth floor is doing most of the work of deciding how many features a sample shows.

Per-run QC

  • 16S identity 84.8% alignment call per run
  • Q30 rate 89.4% mean Q 37.1
  • Amplicon V4 primers present
  • PhiX 0.0% control spike-in

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

Diversity

Shannon
4.98
Simpson
0.986
Evenness
0.865
Chao1
361

Median across samples. Observed richness ranges 122 to 1,152.

Feature prevalence

0 of 7,412 features

present in at least half of the 19 samples (0.0%). 7,355 features appear in one sample only, which is the long tail rarefaction is fighting.

Ordination

pc1 pc2

One point per sample, 19 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 · 8.0%

  • shannon 0.9%
  • observed 0.7%
  • chao1 0.7%
  • reads 0.6%

pc2 · 6.0%

  • reads 61.5%
  • observed 26.8%
  • chao1 26.8%
  • pH 7.8%

pc3 · 5.6%

  • pH 2.1%
  • reads 0.8%
  • observed 0.7%
  • chao1 0.7%

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
6.2 19 samples

Median Shannon 4.983 across the release; observed richness runs 122 to 1152.

Bray-Curtis dissimilarity

19 x 19, darker is closer

Sample order is the release order, 19 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 = 2 silhouette 0.331

  • state 0 18 samples
  • state 1 1 samples

Clustered on the centred log-ratio of the top 200 features; 19 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 0.040

Joint R2 0.040, 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 0.053p 0.908

    Hellinger-scaled, 1 dummy predictors over 19 samples. The constraint explains 5.3% of the community inertia, -0.003 adjusted.

    CCA · p 0.709

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

    Co-occurrence network

    100 nodes · 684 edges

    positive
    684
    negative
    0
    density
    0.138
    components
    14
    mean degree
    13.7

    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.

      Similar studies

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      65 samples

      Ranked from the released tables: genus composition as Bray-Curtis similarity, shared environment and method terms, the distance between sample centroids, and authors shared with the linked publication.

      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 PRJNA254742

      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/PRJNA254742-20260926/ once hosting is wired. Until then the links point at a placeholder base URL.

      Samples

      19 samples
      Sample Collected group Reads Features Shannon State
      SAMN02906678 2012 3,878 361 5.559 0
      SAMN02906679 2012 5,839 138 4.568 0
      SAMN02906680 2012 7,413 131 2.911 0
      SAMN02906681 2012 4,744 144 4.303 0
      SAMN02906682 2012 6,820 482 5.197 0
      SAMN02906683 2012 7,405 767 6.171 0
      SAMN02906684 2012 4,976 122 4.46 0
      SAMN02906685 2012 6,772 124 4.438 0
      SAMN02906686 2012 11,216 328 4.754 0
      SAMN02906687 2012 7,989 502 5.729 0
      SAMN02906688 2012 10,809 445 4.905 0
      SAMN02906689 2012 8,781 417 4.957 0
      SAMN02906690 2012 31,470 1,152 6.078 1
      SAMN02906691 2012 11,467 236 3.861 0
      SAMN02906692 2012 9,057 461 5.303 0
      SAMN02906693 2012 9,496 304 4.988 0
      SAMN02906694 2012 7,243 557 5.957 0
      SAMN02906695 2012 10,145 445 5.196 0
      SAMN02906696 2012 13,842 353 4.983 0

      click a column head to sort