SJ1 Metagenome
Andrew St. James, Elisha WC, Zach Crockett
Generated July 8, 2020

Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions

Andrew R. St. James* and Ruth E. Richardson

*Author/Owner of KBase Narratives

This Narrative is part of a collection used in a single publication. The paper took a metagnomic and metatranscriptomic approach to examine a bioreactor's response to the presence of sulfate, which reduces the production of methane, a valuable product, while producing hydrogen sulfide, a corrosive contaminant.

This Narrative collection has been created to highlight the types of analyses done for this publication. They are as follows (in order):

Please cite: Andrew R St. James, Ruth E Richardson. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions, FEMS Microbiology Ecology, Volume 96, Issue 5, May 2020, https://doi.org/10.1093/femsec/fiaa050.

Workflow Narrative 1: Metagenomic Analysis

Background

Discussion of paper

In this Narrative, genomic DNA reads from the SJ1 sample were assembled, binned, and annotated into MAGs which were used for further analysis in the SJ1 Metatranscriptome Narrative. SJ1 is the parent bioreactor, from which samples were taken for this analysis. The MAGs created in this Narrative were named based on the bin number and taxonomy to which they were assigned (e.g., 047_Deltaproteobacteria_SJ1 was an identified Deltaproteobacteria from bin 047 of the SJ1 metagenome).

For a more complete summary of the publication, please see this Narrative.

Metadata about the sequencing libraries is found in the following table:

Sequencing Library GOLD analysis project ID # Reads (post-QC) # Contigs N50
SJ1 Metagenome Ga0228535 222,599,058 212,269 2,212
SJ1S Metagenome Ga0228536 196,244,686 171,234 2,141
‘Starvation’ Metatranscriptome Ga0232079 30,039,006 — —
‘Control’ Metatranscriptome (6 h) Ga0232080 62,907,116 — —
‘Control’ Metatranscriptome (24 h) Ga0247507 66,383,206 — —
‘Control’ Metatranscriptome (48 h) Ga0232081 49,369,646 — —
‘Sulfate Provision’ Metatranscriptome (6 h) Ga0232082 69,051,286 — —
‘Sulfate Provision’ Metatranscriptome (24 h) Ga0247508 61,969,624 — —
‘Sulfate Provision’ Metatranscriptome (48 h) Ga0247509 50,036,086 — —

Preparation

Sequencing was performed at JGI using standard pipelines. QC-filtered reads were generated and upload to KBase here.

Narrative Table of Contents

  1. Assembly with metaSPAdes
  2. Binning with MaxBin2
  3. Extracting binned contigs as assemblies
  4. Assess bin quality with CheckM
  5. Annotate assemblies with RAST
  6. Build Genome Set and Annotate
  7. Build Metabolic Model
  8. Supplementary Information
from biokbase.narrative.jobs.jobmanager import JobManager
JobManager().get_job('5a78889be4b07981a2f9253e')
Out[ ]:
from biokbase.narrative.jobs.jobmanager import JobManager
JobManager().get_job('5a79edfae4b07981a2f926d6')
Out[ ]:
from biokbase.narrative.jobs.jobmanager import JobManager
JobManager().get_job('5a78a14fe4b07981a2f92586')
Out[3]:

Assembly with metaSPAdes

QC-filtered reads for the SJ1 and SJ1S metagenomes sequenced at JGI were uploaded and assembled with metaSPAdes using default minimum contig length (2000), shown below.

Assemble with metaSPAdes - v3.11.1
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 23h 13m 57s.
Objects
Created Object Name Type Description
SJ1_SPAdes.contigs Assembly Assembled contigs
Report
Summary
Assembly saved to: ars395:narrative_1517848109205/SPAdes.contigs Assembled into 23530 contigs. Avg Length: 13264.2641734 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 23143 -- 2000.0 to 138771.7 bp 297 -- 138771.7 to 275543.4 bp 55 -- 275543.4 to 412315.1 bp 24 -- 412315.1 to 549086.8 bp 6 -- 549086.8 to 685858.5 bp 2 -- 685858.5 to 822630.2 bp 1 -- 822630.2 to 959401.9 bp 0 -- 959401.9 to 1096173.6 bp 1 -- 1096173.6 to 1232945.3 bp 1 -- 1232945.3 to 1369717.0 bp
Links
Assemble with metaSPAdes - v3.11.1
Assemble metagenomic reads using the SPAdes assembler.
This app completed without errors in 5h 52m 37s.
Objects
Created Object Name Type Description
SJ1S_SPAdes.contigs Assembly Assembled contigs
Report
Summary
Assembly saved to: ars395:narrative_1517848109205/SJ1S_SPAdes.contigs Assembled into 19605 contigs. Avg Length: 11303.4478959 bp. Contig Length Distribution (# of contigs -- min to max basepairs): 19477 -- 2000.0 to 194355.6 bp 102 -- 194355.6 to 386711.2 bp 17 -- 386711.2 to 579066.8 bp 5 -- 579066.8 to 771422.4 bp 2 -- 771422.4 to 963778.0 bp 0 -- 963778.0 to 1156133.6 bp 0 -- 1156133.6 to 1348489.2 bp 0 -- 1348489.2 to 1540844.8 bp 1 -- 1540844.8 to 1733200.4 bp 1 -- 1733200.4 to 1925556.0 bp
Links

Binning with MaxBin2

Assembled metagenomic reads were binned using MaxBin2.

MaxBin2 Contig Binning - v2.2.3
Bin assembled metagenomic contigs
This app completed without errors in 6h 46m 37s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • maxbin_result.zip - File(s) generated by MaxBin2 App
  • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
Output from MaxBin2 Contig Binning - v2.2.3
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
MaxBin2 Contig Binning - v2.2.3
Bin assembled metagenomic contigs
This app completed without errors in 4h 23m 14s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • maxbin_result.zip - File(s) generated by MaxBin2 App
Output from MaxBin2 Contig Binning - v2.2.3
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
MaxBin2 Contig Binning - v2.2.3
Bin assembled metagenomic contigs
This app completed without errors in 8h 21m 20s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • maxbin_result.zip - File(s) generated by MaxBin2 App
  • Bin.marker.pdf - Visualization of the marker by MaxBin2 App
Output from MaxBin2 Contig Binning - v2.2.3
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Output from MaxBin2 Contig Binning - v2.2.3
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057

Extracting Binned Contigs as Assemblies

The binned contigs were extracted as MAG assemblies using Extract Bins as Assemblies from BinnedContigs, and then an AssemblySet was generated to group the MAGs.

Extract Bins as Assemblies from BinnedContigs - v1.0.0
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 3m 33s.
Summary
Job Finished Generated Assembly Reference: 28057/12/1
Extract Bins as Assemblies from BinnedContigs - v1.0.0
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 7m 16s.
Summary
Job Finished Generated Assembly Reference: 28057/37/1, 28057/38/1, 28057/39/1, 28057/40/1, 28057/41/1, 28057/42/1, 28057/43/1, 28057/44/1, 28057/45/1, 28057/46/1, 28057/47/1, 28057/48/1, 28057/49/1, 28057/50/1, 28057/51/1, 28057/52/1
Extract Bins as Assemblies from BinnedContigs - v1.0.0
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 3m 10s.
Summary
Job Finished Generated Assembly Reference: 28057/29/1
Extract Bins as Assemblies from BinnedContigs - v1.0.0
Extract a bin as an Assembly from a BinnedContig dataset
This app completed without errors in 2m 3s.
Summary
Job Finished Generated Assembly Reference: 28057/25/1
Build AssemblySet - v1.0.1
Allows user to create an AssemblySet
This app completed without errors in 9s.
Objects
Created Object Name Type Description
SJ1_SRB_Bins AssemblySet KButil_Build_AssemblySet
Summary
assembly objs in output set SJ1_SRB_Bins: 16

Assess Bin Quality with CheckM

The extracted bins were then analyzed with CheckM and compared with Compared Assembled Contig Distributions.

Assess Genome Quality with CheckM - v1.0.8
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies
This app completed without errors in 2h 22m 7s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Assess Genome Quality with CheckM - v1.0.8
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies
This app completed without errors in 2h 11m 24s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Assess Genome Quality with CheckM - v1.0.8
Runs the CheckM lineage workflow to assess the genome quality of isolates, single cells, or genome bins from metagenome assemblies
This app completed without errors in 1h 33m 52s.
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • full_output.zip - Full output of CheckM
  • plots.zip - Output plots from CheckM
Compare Assembled Contig Distributions - v1.1.2
View distributions of contig characteristics for different assemblies
This app completed without errors in 3m 51s.
Report
Summary
ASSEMBLY STATS for Bin.066.fastaSJ1_066_assembly Len longest contig: 81856 bp N50 (L50): 5592 (25) N75 (L75): 3020 (80) N90 (L90): 2380 (127) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 0 Num contigs >= 10000 bp: 12 Num contigs >= 1000 bp: 166 Num contigs >= 500 bp: 166 Num contigs >= 1 bp: 166 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 0 bp Len contigs >= 10000 bp: 333367 bp Len contigs >= 1000 bp: 857907 bp Len contigs >= 500 bp: 857907 bp Len contigs >= 1 bp: 857907 bp ASSEMBLY STATS for Bin.103.fastaSJ1_103_assembly Len longest contig: 70934 bp N50 (L50): 18500 (69) N75 (L75): 10414 (140) N90 (L90): 5450 (217) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 0 Num contigs >= 10000 bp: 143 Num contigs >= 1000 bp: 324 Num contigs >= 500 bp: 324 Num contigs >= 1 bp: 324 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 0 bp Len contigs >= 10000 bp: 3011584 bp Len contigs >= 1000 bp: 3970637 bp Len contigs >= 500 bp: 3970637 bp Len contigs >= 1 bp: 3970637 bp ASSEMBLY STATS for Bin.077.fastaSJ1_077_assembly Len longest contig: 42961 bp N50 (L50): 7797 (95) N75 (L75): 4980 (184) N90 (L90): 2929 (272) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 0 Num contigs >= 10000 bp: 51 Num contigs >= 1000 bp: 363 Num contigs >= 500 bp: 363 Num contigs >= 1 bp: 363 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 0 bp Len contigs >= 10000 bp: 748142 bp Len contigs >= 1000 bp: 2248572 bp Len contigs >= 500 bp: 2248572 bp Len contigs >= 1 bp: 2248572 bp ASSEMBLY STATS for Bin.071.fastaSJ1_071_assembly Len longest contig: 188670 bp N50 (L50): 47623 (27) N75 (L75): 22922 (54) N90 (L90): 5258 (98) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 3 Num contigs >= 10000 bp: 81 Num contigs >= 1000 bp: 230 Num contigs >= 500 bp: 230 Num contigs >= 1 bp: 230 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 446419 bp Len contigs >= 10000 bp: 3263312 bp Len contigs >= 1000 bp: 3759395 bp Len contigs >= 500 bp: 3759395 bp Len contigs >= 1 bp: 3759395 bp ASSEMBLY STATS for Bin.040.fastaSJ1_040_assembly Len longest contig: 264099 bp N50 (L50): 199199 (7) N75 (L75): 89600 (12) N90 (L90): 54165 (18) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 11 Num contigs >= 10000 bp: 27 Num contigs >= 1000 bp: 32 Num contigs >= 500 bp: 32 Num contigs >= 1 bp: 32 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 2076385 bp Len contigs >= 10000 bp: 2788651 bp Len contigs >= 1000 bp: 2807587 bp Len contigs >= 500 bp: 2807587 bp Len contigs >= 1 bp: 2807587 bp ASSEMBLY STATS for Bin.059.fastaSJ1_059_assembly Len longest contig: 89387 bp N50 (L50): 28040 (33) N75 (L75): 15835 (68) N90 (L90): 7427 (109) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 0 Num contigs >= 10000 bp: 92 Num contigs >= 1000 bp: 182 Num contigs >= 500 bp: 182 Num contigs >= 1 bp: 182 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 0 bp Len contigs >= 10000 bp: 2452792 bp Len contigs >= 1000 bp: 2878524 bp Len contigs >= 500 bp: 2878524 bp Len contigs >= 1 bp: 2878524 bp ASSEMBLY STATS for Bin.047.fastaSJ1_047_assembly Len longest contig: 134731 bp N50 (L50): 48354 (22) N75 (L75): 30873 (45) N90 (L90): 12679 (71) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 4 Num contigs >= 10000 bp: 76 Num contigs >= 1000 bp: 130 Num contigs >= 500 bp: 130 Num contigs >= 1 bp: 130 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 468492 bp Len contigs >= 10000 bp: 3173567 bp Len contigs >= 1000 bp: 3456341 bp Len contigs >= 500 bp: 3456341 bp Len contigs >= 1 bp: 3456341 bp ASSEMBLY STATS for Bin.001.fastaSJ1_001_assembly Len longest contig: 536931 bp N50 (L50): 203289 (7) N75 (L75): 101772 (13) N90 (L90): 62553 (21) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 14 Num contigs >= 10000 bp: 30 Num contigs >= 1000 bp: 34 Num contigs >= 500 bp: 34 Num contigs >= 1 bp: 34 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 3001003 bp Len contigs >= 10000 bp: 3829570 bp Len contigs >= 1000 bp: 3858682 bp Len contigs >= 500 bp: 3858682 bp Len contigs >= 1 bp: 3858682 bp ASSEMBLY STATS for Bin.067.fastaSJ1_067_assembly Len longest contig: 210078 bp N50 (L50): 60620 (12) N75 (L75): 43067 (25) N90 (L90): 26316 (35) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 6 Num contigs >= 10000 bp: 45 Num contigs >= 1000 bp: 57 Num contigs >= 500 bp: 57 Num contigs >= 1 bp: 57 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 858592 bp Len contigs >= 10000 bp: 2464751 bp Len contigs >= 1000 bp: 2510528 bp Len contigs >= 500 bp: 2510528 bp Len contigs >= 1 bp: 2510528 bp ASSEMBLY STATS for Bin.058.fastaSJ1_058_assembly Len longest contig: 428836 bp N50 (L50): 145843 (9) N75 (L75): 77706 (17) N90 (L90): 41365 (27) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 14 Num contigs >= 10000 bp: 40 Num contigs >= 1000 bp: 58 Num contigs >= 500 bp: 58 Num contigs >= 1 bp: 58 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 2634730 bp Len contigs >= 10000 bp: 3726320 bp Len contigs >= 1000 bp: 3816427 bp Len contigs >= 500 bp: 3816427 bp Len contigs >= 1 bp: 3816427 bp ASSEMBLY STATS for Bin.008.fastaSJ1_008_assembly Len longest contig: 253756 bp N50 (L50): 50382 (15) N75 (L75): 23416 (38) N90 (L90): 13209 (62) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 6 Num contigs >= 10000 bp: 67 Num contigs >= 1000 bp: 118 Num contigs >= 500 bp: 118 Num contigs >= 1 bp: 118 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 902504 bp Len contigs >= 10000 bp: 2806892 bp Len contigs >= 1000 bp: 3056831 bp Len contigs >= 500 bp: 3056831 bp Len contigs >= 1 bp: 3056831 bp ASSEMBLY STATS for Bin.010.fastaSJ1_010_assembly Len longest contig: 1146498 bp N50 (L50): 289052 (3) N75 (L75): 162708 (8) N90 (L90): 95454 (12) Num contigs >= 1000000 bp: 1 Num contigs >= 100000 bp: 11 Num contigs >= 10000 bp: 18 Num contigs >= 1000 bp: 22 Num contigs >= 500 bp: 22 Num contigs >= 1 bp: 22 Len contigs >= 1000000 bp: 1146498 bp Len contigs >= 100000 bp: 3545841 bp Len contigs >= 10000 bp: 4001556 bp Len contigs >= 1000 bp: 4019044 bp Len contigs >= 500 bp: 4019044 bp Len contigs >= 1 bp: 4019044 bp ASSEMBLY STATS for Bin.015.fastaSJ1_015_assembly Len longest contig: 516047 bp N50 (L50): 156613 (11) N75 (L75): 82933 (22) N90 (L90): 20859 (42) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 18 Num contigs >= 10000 bp: 59 Num contigs >= 1000 bp: 123 Num contigs >= 500 bp: 123 Num contigs >= 1 bp: 123 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 3717104 bp Len contigs >= 10000 bp: 5128409 bp Len contigs >= 1000 bp: 5409367 bp Len contigs >= 500 bp: 5409367 bp Len contigs >= 1 bp: 5409367 bp ASSEMBLY STATS for Bin.041.fastaSJ1_041_assembly Len longest contig: 379539 bp N50 (L50): 160372 (7) N75 (L75): 119230 (13) N90 (L90): 53440 (19) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 15 Num contigs >= 10000 bp: 28 Num contigs >= 1000 bp: 40 Num contigs >= 500 bp: 40 Num contigs >= 1 bp: 40 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 2886430 bp Len contigs >= 10000 bp: 3456817 bp Len contigs >= 1000 bp: 3507674 bp Len contigs >= 500 bp: 3507674 bp Len contigs >= 1 bp: 3507674 bp ASSEMBLY STATS for Bin.044.fastaSJ1_044_assembly Len longest contig: 370317 bp N50 (L50): 50489 (17) N75 (L75): 28416 (38) N90 (L90): 14783 (62) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 5 Num contigs >= 10000 bp: 70 Num contigs >= 1000 bp: 114 Num contigs >= 500 bp: 114 Num contigs >= 1 bp: 114 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 817223 bp Len contigs >= 10000 bp: 3034509 bp Len contigs >= 1000 bp: 3252270 bp Len contigs >= 500 bp: 3252270 bp Len contigs >= 1 bp: 3252270 bp ASSEMBLY STATS for Bin.013.fastaSJ1_013_assembly Len longest contig: 555751 bp N50 (L50): 146088 (9) N75 (L75): 76529 (18) N90 (L90): 52844 (26) Num contigs >= 1000000 bp: 0 Num contigs >= 100000 bp: 14 Num contigs >= 10000 bp: 35 Num contigs >= 1000 bp: 51 Num contigs >= 500 bp: 51 Num contigs >= 1 bp: 51 Len contigs >= 1000000 bp: 0 bp Len contigs >= 100000 bp: 2556047 bp Len contigs >= 10000 bp: 3707083 bp Len contigs >= 1000 bp: 3790982 bp Len contigs >= 500 bp: 3790982 bp Len contigs >= 1 bp: 3790982 bp
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/28057
  • key_plot.png
  • key_plot.pdf
  • cumulative_len_plot.png
  • cumulative_len_plot.pdf
  • sorted_contig_lengths.png
  • sorted_contig_lengths.pdf
  • histogram_figures.zip

Annotate

All extracted assembly objects were annotated using the Annotate Microbial Assembly App, which is based on the RAST toolkit.

Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 4m 40s.
Objects
Created Object Name Type Description
103_Desulfovibrio_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 16m 59s.
Objects
Created Object Name Type Description
010_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 15m 46s.
Objects
Created Object Name Type Description
015_Desulfobacteraceae_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 16m 18s.
Objects
Created Object Name Type Description
041_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 12m 13s.
Objects
Created Object Name Type Description
058_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 15m 37s.
Objects
Created Object Name Type Description
067_Peptococcaceae_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 8m 21s.
Objects
Created Object Name Type Description
008_Desulfovibrio_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 3m 12s.
Objects
Created Object Name Type Description
044_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 4m 32s.
Objects
Created Object Name Type Description
047_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 11m 8s.
Objects
Created Object Name Type Description
059_Nitrospiraceae_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 13m 53s.
Objects
Created Object Name Type Description
013_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 3m 29s.
Objects
Created Object Name Type Description
040_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 33m 3s.
Objects
Created Object Name Type Description
071_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 24m 18s.
Objects
Created Object Name Type Description
077_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 4h 6m 59s.
Objects
Created Object Name Type Description
103_Desulfovibrio_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 12m 57s.
Objects
Created Object Name Type Description
066_Deltaproteobacteria_SJ1 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 3m 36s.
Objects
Created Object Name Type Description
001_Desulfovibrio Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 4m 45s.
Objects
Created Object Name Type Description
Bin.097 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 13m 25s.
Objects
Created Object Name Type Description
SJ1_Bin.001_Genome Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app completed without errors in 1h 0m 49s.
Objects
Created Object Name Type Description
Bin.001 Genome Annotated genome
Report
Output from Annotate Microbial Assembly
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app was canceled before completion.
No output found.
Annotate Microbial Assembly
Annotate a bacterial or archaeal assembly using components from the RAST (Rapid Annotations using Subsystems Technology) toolkit (RASTtk).
This app produced errors in 21h 55m 56s.
No output found.

Build and Annotate GenomeSet

Resulting annotated assemblies (genome objects in KBase) were combined into a genome set, and domain annotation was performed on the resulting set.
Then, the annotated genome set was placed into a species tree.

Build GenomeSet - v1.0.1
Allows user to create a GenomeSet
This app completed without errors in 34s.
Objects
Created Object Name Type Description
SJ1_SRB_putative GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set SJ1_SRB_putative: 14
Output from Build GenomeSet - v1.0.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Build GenomeSet - v1.0.1
Allows user to create a GenomeSet
This app completed without errors in 23s.
Objects
Created Object Name Type Description
SJ1_SRB_Bing GenomeSet KButil_Build_GenomeSet
Summary
genomes in output set SJ1_SRB_Bing: 8
Output from Build GenomeSet - v1.0.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057
Annotate Domains in a GenomeSet
Run DomainAnnotation on a Genome Set
This app was canceled before completion.
No output found.
Insert Set of Genomes Into Species Tree
Add a user-provided GenomeSet to a KBase species tree.
This app produced errors in 3m 2s.
No output found.
Output from Insert Set of Genomes Into Species Tree
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057

Build Metabolic Model

An example metabolic model was generated for Bin 001 of the SJ1 sample.

Build Metabolic Model
Generate a draft metabolic model based on an annotated genome.
This app completed without errors in 1m 28s.
Objects
Created Object Name Type Description
SJ1_Bin.001_GenomeModel FBAModel FBAModel-11 SJ1_Bin.001_GenomeModel
SJ1_Bin.001_GenomeModel.gf.0 FBA FBA-13 SJ1_Bin.001_GenomeModel.gf.0
Report
Output from Build Metabolic Model
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/28057

Supplementary Information

The objects contained in this Narrative as well as the key objects used for all analyses in the publication can be viewed and copied for further analysis in the SJ1 Intermediate Files Narrative.

Apps

  1. Annotate Domains in a GenomeSet
    • Altschul SF, Madden TL, Sch ffer AA, Zhang J, Zhang Z, Miller W, et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25: 3389 3402. doi:10.1093/nar/25.17.3389
    • Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, et al. BLAST+: architecture and applications. BMC Bioinformatics. 2009;10: 421. doi:10.1186/1471-2105-10-421
    • Eddy SR. Accelerated Profile HMM Searches. PLOS Computational Biology. 2011;7: e1002195. doi:10.1371/journal.pcbi.1002195
    • Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res. 2016;44: D279 D285. doi:10.1093/nar/gkv1344
    • Haft DH, Selengut JD, Richter RA, Harkins D, Basu MK, Beck E. TIGRFAMs and Genome Properties in 2013. Nucleic Acids Res. 2013;41: D387 D395. doi:10.1093/nar/gks1234
    • Letunic I, Bork P. 20 years of the SMART protein domain annotation resource. Nucleic Acids Res. 2018;46: D493 D496. doi:10.1093/nar/gkx922
    • Letunic I, Doerks T, Bork P. SMART: recent updates, new developments and status in 2015. Nucleic Acids Res. 2015;43: D257-260. doi:10.1093/nar/gku949
    • Marchler-Bauer A, Bo Y, Han L, He J, Lanczycki CJ, Lu S, et al. CDD/SPARCLE: functional classification of proteins via subfamily domain architectures. Nucleic Acids Res. 2017;45: D200 D203. doi:10.1093/nar/gkw1129
    • Selengut JD, Haft DH, Davidsen T, Ganapathy A, Gwinn-Giglio M, Nelson WC, et al. TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes. Nucleic Acids Res. 2007;35: D260-264. doi:10.1093/nar/gkl1043
    • Tatusov RL, Koonin EV, Lipman DJ. A Genomic Perspective on Protein Families. Science. 1997;278: 631 637. doi:10.1126/science.278.5338.631
  2. Annotate Microbial Assembly
    • Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: Rapid Annotations using Subsystems Technology. BMC Genomics. 2008;9: 75. doi:10.1186/1471-2164-9-75
    • Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5: 8365. doi:10.1038/srep08365
    • Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206-214. doi:10.1093/nar/gkt1226
  3. Assemble Reads with metaSPAdes - v3.13.0
    • Nurk S, Meleshko D, Korobeynikov A, Pevzner PA. metaSPAdes: a new versatile metagenomic assembler. Genome Res. 2017; 27:824 834. doi: 10.1101/gr.213959.116
  4. Assess Genome Quality with CheckM - v1.0.18
    • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25: 1043 1055. doi:10.1101/gr.186072.114
    • CheckM source:
    • Additional info:
  5. Bin Contigs using MaxBin2 - v2.2.4
    • Wu Y-W, Simmons BA, Singer SW. MaxBin 2.0: an automated binning algorithm to recover genomes from multiple metagenomic datasets. Bioinformatics. 2016;32: 605 607. doi:10.1093/bioinformatics/btv638 (2) 1. Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
    • Wu Y-W, Tang Y-H, Tringe SG, Simmons BA, Singer SW. MaxBin: an automated binning method to recover individual genomes from metagenomes using an expectation-maximization algorithm. Microbiome. 2014;2: 26. doi:10.1186/2049-2618-2-26
    • Maxbin2 source:
    • Maxbin source:
  6. Build AssemblySet - v1.0.1
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  7. Build GenomeSet - v1.0.1
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  8. Build Metabolic Model
    • [1] Henry CS, DeJongh M, Best AA, Frybarger PM, Linsay B, Stevens RL. High-throughput generation, optimization and analysis of genome-scale metabolic models. Nat Biotechnol. 2010;28: 977 982. doi:10.1038/nbt.1672
    • [2] Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42: D206 D214. doi:10.1093/nar/gkt1226
    • [3] Latendresse M. Efficiently gap-filling reaction networks. BMC Bioinformatics. 2014;15: 225. doi:10.1186/1471-2105-15-225
    • [4] Dreyfuss JM, Zucker JD, Hood HM, Ocasio LR, Sachs MS, Galagan JE. Reconstruction and Validation of a Genome-Scale Metabolic Model for the Filamentous Fungus Neurospora crassa Using FARM. PLOS Computational Biology. 2013;9: e1003126. doi:10.1371/journal.pcbi.1003126
    • [5] Mahadevan R, Schilling CH. The effects of alternate optimal solutions in constraint-based genome-scale metabolic models. Metab Eng. 2003;5: 264 276.
  9. Compare Assembled Contig Distributions - v1.1.2
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  10. Extract Bins as Assemblies from BinnedContigs - v1.0.2
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  11. Insert Set of Genomes Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490