Lactobacillus (ID 608517) - BioProject

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Accession: PRJNA608517 ID: 608517

Lactobacillus

The Lactobacillus genus, a use case for Bactopia.

This project includes all 1,664 publicly available SRA samples marked as a part of the Lactobacillus genus with Illumina technology sequencing that were used in our demonstration of Bactopia. (2020-02-24)

Accession	PRJNA608517
Type	Umbrella project
Submission	Registration date: 24-Feb-2020 Emory University
Related Resources	Bactopia Github Repo Bactopia Documentation
Relevance	Use case of a the bacterial genomics workflow, Bactopia.

Project Data:

Resource Name	Number of Links
Sequence data
Nucleotide (total)	38762340
WGS master	326122
Genomic DNA	120433
Genomic RNA	279
Transcript	5506
SRA Experiments	33599
Protein Sequences	292947276
Publications
PubMed	46
PMC	33
Other datasets
BioSample	397812
Assembly	368313

SRA Data Details

Parameter	Value
Data volume, Gbases	23,587
Data volume, Tbytes	16.25

Lactobacillus encompasses the following 217 sub-projects:

Project Type

Number of Projects

Genome sequencing

Highest level of assembly :

Complete genome
Chromosomes
Scaffolds
Contigs
SRA or Trace
Total

16
5
69
44
65
199

BioProject accession	Assembly level	Name	Title
PRJNA270968	Scaffolds	Apilactobacillus apinorum	Lactobacillus apinorum Genome sequencing (Uppsala university)
PRJNA270961	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAan Genome sequencing and assembly (Uppsala university)
PRJNA270962	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAce Genome sequencing and assembly (Uppsala university)
PRJNA270963	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAdo Genome sequencing and assembly (Uppsala university)
PRJNA270964	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAfl Genome sequencing and assembly (Uppsala university)

List all 199 'Genome sequencing' projects...

BioProject accession	Assembly level	Name	Title
PRJNA270968	Scaffolds	Apilactobacillus apinorum	Lactobacillus apinorum Genome sequencing (Uppsala university)
PRJNA270961	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAan Genome sequencing and assembly (Uppsala university)
PRJNA270962	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAce Genome sequencing and assembly (Uppsala university)
PRJNA270963	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAdo Genome sequencing and assembly (Uppsala university)
PRJNA270964	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAfl Genome sequencing and assembly (Uppsala university)
PRJNA270965	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAko Genome sequencing and assembly (Uppsala university)
PRJNA270966	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAla Genome sequencing and assembly (Uppsala university)
PRJNA270967	Scaffolds	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:Fhon2 Genome sequencing and assembly (Uppsala university)
PRJNA270969	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAni Genome sequencing and assembly (Uppsala university)
PRJNA270970	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LAnu Genome sequencing and assembly (Uppsala university)
PRJNA270972	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LMbe Genome sequencing and assembly (Uppsala university)
PRJNA270973	Contigs	Apilactobacillus kunkeei	Apilactobacillus kunkeei strain:LMbo Genome sequencing and assembly (Uppsala university)
PRJNA542049	Contigs	Apilactobacillus kunkeei	Lactobacillus kunkeei strain NN5 Genome sequencing and assembly (University of Applied Sciences...)
PRJNA542050	Contigs	Apilactobacillus kunkeei	Lactobacillus kunkeei strain NN17 Genome sequencing and assembly (University of Applied Sciences...)
PRJNA542054	Contigs	Apilactobacillus kunkeei	Lactobacillus kunkeei strain NN20 Genome sequencing and assembly (University of Applied Sciences...)
PRJNA270974	Contigs	Apilactobacillus kunkeei DSM 12361 = ATCC 700308	Apilactobacillus kunkeei DSM 12361 = ATCC 700308 strain:YH-15 Genome sequencing and assembly (Uppsala university)
PRJNA227106	Contigs	Apilactobacillus kunkeei EFB6	Apilactobacillus kunkeei EFB6 Genome sequencing and assembly (Georg-August-University Goettingen,...)
PRJDB6480	Contigs	Apilactobacillus micheneri	Draft Genome Sequence of Lactobacillus kosoensis NBRC 113063 (Department of Biotechnology...)
PRJNA544527	Scaffolds	BIO-ML: The Broad Institute-OpenBiome Microbiome Library enables mechanistic studies with isolates, genomes, and longitudinal metagenomics and metabolomic data	BIO-ML: The Broad Institute-OpenBiome Microbiome Library enables mechanistic studies with isolates, genomes, and longitudinal metagenomics and metabolomic data (Massachusetts Institute of...)
PRJEB22252	Chromosomes	Baby_Biome_Study_gastrointestinal_bacterial_genomes	Baby_Biome_Study_gastrointestinal_bacterial_genomes (Wellcome Sanger Institute)
PRJDB5206	SRA or Trace	Bacteria	Genome sequencing project (National Institute of Technology...)
PRJNA316969	Complete genome	Bacteria	Female Urinary Microbiota Genome Sequencing (Loyola University Chicago)
PRJNA379934	Scaffolds	Bacteria	ATCC bacterial species genome sequencing and assembly (Loyola University Chicago)
PRJNA474823	Scaffolds	Bacteria	Lactic acid bacteria of Slovakian bryndza cheese. (Faculty of Natural Sciences...)
PRJNA474907	Contigs	Bacteria	Genome sequencing and assembly - library of cultured bacterial species from laboratory mouse gut microbiota from the University of Toronto (University of Toronto)
PRJNA493554	Scaffolds	Bacteria	Probiogenomics (Unique Biotech Limited)
PRJNA496358	Contigs	Bacteria	Genomes of 49 bacteria species isolated from stool from healthy individuals (Broad Institute)
PRJNA577465	Scaffolds	Bacteria	Bacterial species found as contaminants in Brazilian ethanol industrial fermentations (Univesity of Sao Paulo)
PRJNA267549	Scaffolds	Bacterial isolates from intensive care units	Bacterial isolates from intensive care units (University of Washington)
PRJNA257185	Scaffolds	Bombilactobacillus mellifer	Bombilactobacillus mellifer strain:Bin4 Genome sequencing and assembly (Uppsala university)
PRJNA257182	Scaffolds	Bombilactobacillus mellis	Bombilactobacillus mellis strain:Hon2 Genome sequencing and assembly (Uppsala university)
PRJNA184888	SRA or Trace	Clinical microbiology Genome sequencing	Clinical microbiology Genome sequencing (The Methodist Hospital Research...)
PRJEB3012	Scaffolds	Clostridium difficile 078 diversity	Clostridium difficile 078 diversity (Wellcome Sanger Institute)
PRJNA234998	SRA or Trace	Companilactobacillus paralimentarius DSM 13238 = JCM 10415	Companilactobacillus paralimentarius DSM 13238 = JCM 10415 Genome sequencing (DOE Joint Genome Institute)
PRJEB21025	Contigs	Comparative Genomics Lactobacillus casei group	Large-Scale Phylogenomics of the Lactobacillus casei Group Highlights Taxonomic Inconsistencies and Reveals Novel Clade-Associated Features (UANTW)
PRJNA484967	Scaffolds	Comparative Genomics of Non-Corbiculate Bee and Flower Associated Lactobacillus	Comparative Genomics of Non-Corbiculate Bee and Flower Associated Lactobacillus (University of California,...)
PRJNA547620	SRA or Trace	Comparison of mother-daughter vaginal Lactobacillus crispatus genome sequences	Comparison of mother-daughter vaginal Lactobacillus crispatus genome sequences (University of Michigan)
PRJNA543187	Complete genome	Development & evaluation of Morphoseq synthetic long read sequencing technology	Development & evaluation of Morphoseq synthetic long read sequencing technology (University of Technology...)
PRJNA306257	Complete genome	Drosophila melanogaster	Isolated intestinal bacteria from Drosophila melanogaster (University of Alberta)
PRJNA400793	SRA or Trace	Effect of high salt diet on gut microbiome of mice	Effect of high salt diet on gut microbiome of mice (MIT)
PRJNA185584	Scaffolds	Eggerthia catenaformis OT 569 = DSM 20559	Eggerthia catenaformis DSM 20559 (DOE Joint Genome Institute)
PRJNA231221	Complete genome	FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science	FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science (US Food and Drug Administration)
PRJNA1128260	Contigs	FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science	FDA-ARGOS is a database with public quality-controlled reference genomes for diagnostic use and regulatory science (NCBI)
PRJNA235017	SRA or Trace	Fructilactobacillus lindneri DSM 20690 = JCM 11027	Fructilactobacillus lindneri DSM 20690 = JCM 11027 Genome sequencing (DOE Joint Genome Institute)
PRJNA185359	Scaffolds	Furfurilactobacillus rossiae DSM 15814	Lactobacillus rossiae DSM 15814 (DOE Joint Genome Institute)
PRJEB8721	Scaffolds	Global_population_genomics_of_Campylobacter_fetus	Global_population_genomics_of_Campylobacter_fetus (Wellcome Sanger Institute)
PRJNA562050	SRA or Trace	LGG isolates from capsules and blood	LGG isolates from capsules and blood (Technion)
PRJNA342061	SRA or Trace	Lacticaseibacillus casei	Lacticaseibacillus casei strain:Zhang Raw sequence reads (Inner Mongolia Agricultural...)
PRJNA68459	Contigs	Lacticaseibacillus casei 21/1	Comparative genomics of Lactobacillus casei (University of Wisconsin-Madison,...)
PRJNA218804	Scaffolds	Lacticaseibacillus casei A2-362	Lacticaseibacillus casei A2-362 Genome sequencing and assembly (DOE Joint Genome Institute)
PRJNA165565	Contigs	Lacticaseibacillus paracasei	Lacticaseibacillus paracasei strain:UW4 Genome sequencing and assembly (DOE Joint Genome Institute)
PRJNA217366	Contigs	Lacticaseibacillus paracasei	Lacticaseibacillus paracasei strain:12A Genome sequencing and assembly (DOE Joint Genome Institute)
PRJNA255080	Contigs	Lacticaseibacillus paracasei	Detailed Comparative Genomics of Lactobacillus paracasei Strains with Re-analyzed Lbs2 Strain Reveals a Small Core Proteome with Potential Probiotic Properties (Indian Institute of Chemical...)
PRJNA302242	Scaffolds	Lacticaseibacillus paracasei	Lacticaseibacillus paracasei strain:BM-LC14617 Genome sequencing and assembly (South China University of...)
PRJNA348789	Scaffolds	Lacticaseibacillus rhamnosus	Sequencing Lactobacillus rhamnosus strains of dairy origins (The University of Queensland)
PRJNA185406	SRA or Trace	Lacticaseibacillus rhamnosus GG	Lacticaseibacillus rhamnosus GG strain:ATCC 53103 Genome sequencing (VU University)
PRJNA258500	SRA or Trace	Lacticaseibacillus rhamnosus GG	Lacticaseibacillus rhamnosus GG strain:GG Genome sequencing (University of Helsinki)
PRJNA305242	SRA or Trace	Lacticaseibacillus rhamnosus GG	Lactobacillus rhamnosus GG derivative genome sequencing (University of Helsinki)
PRJNA219157	Scaffolds	Lactiplantibacillus fabifermentans T30PCM01	Lactiplantibacillus fabifermentans T30PCM01 Genome sequencing and assembly (University of Padova)
PRJNA492883	Scaffolds	Lactiplantibacillus pentosus	Genome sequences of five Lactobacillus pentosus strains from brines of olives (Instituto de la Grasa-CSIC)
PRJNA247440	SRA or Trace	Lactiplantibacillus plantarum	Lactobacillus plantarum ATCC 8014 LP8_5H Genome sequencing, assembly and annotation (Massey University)
PRJNA247441	SRA or Trace	Lactiplantibacillus plantarum	Lactobacillus plantarum ATCC 8014 LP8_4H Genome sequencing, assembly and annotation (Massey University)
PRJNA247442	SRA or Trace	Lactiplantibacillus plantarum	Lactobacillus plantarum ATCC 8014 LP8_1L Genome sequencing, assembly and annotation (Massey University)
PRJNA247443	Scaffolds	Lactiplantibacillus plantarum	Lactobacillus plantarum ATCC 8014 WT Genome sequencing, assembly and annotation (Massey University)
PRJNA258355	SRA or Trace	Lactiplantibacillus plantarum	Lactobacillus plantarum 965 Genome sequencing, assembly and annotation (Massey University)
PRJNA291681	Complete genome	Lactiplantibacillus plantarum	Lactobacillus plantarum ZS2058 genome sequencing (Jiangnan University)
PRJNA296751	Scaffolds	Lactiplantibacillus plantarum	Lactiplantibacillus plantarum strain:Kanjika2007 Genome sequencing and assembly (CSIR-CFTRI)
PRJNA381357	Complete genome	Lactiplantibacillus plantarum	Lactiplantibacillus plantarum Genome sequencing (Beijing Academy of Agriculture...)
PRJNA397632	SRA or Trace	Lactiplantibacillus plantarum	Lactiplantibacillus plantarum strain:IMAU 10120v Raw sequence reads (Inner Mongolia Agricultural...)
PRJNA525939	SRA or Trace	Lactiplantibacillus plantarum	Lactiplantibacillus plantarum Genome sequencing and assembly (KAGOME Co.,Ltd. Innovation...)
PRJNA247439	SRA or Trace	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Lactobacillus plantarum subsp. plantarum ATCC 14917 WT Genome sequencing, assembly and annotation (Massey University)
PRJNA247444	SRA or Trace	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Lactobacillus plantarum subsp. plantarum ATCC 14917 LP1_4H Genome sequencing, assembly and annotation (Massey University)
PRJNA247445	SRA or Trace	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Lactobacillus plantarum subsp. plantarum ATCC 14917 LP1_3L Genome sequencing, assembly and annotation (Massey University)
PRJNA247446	SRA or Trace	Lactiplantibacillus plantarum subsp. plantarum ATCC 14917 = JCM 1149 = CGMCC 1.2437	Lactobacillus plantarum subsp. plantarum ATCC 14917 LP1_2H Genome sequencing, assembly and annotation (Massey University)
PRJDB1101	Scaffolds	Lactobacillales	Genome Project of Lactic Acid Bacteria Beneficial for Fermentation of Rice Grain Silage (National Agriculture and...)
PRJNA222257	Scaffolds	Lactobacillus	Lactobacillus Multispecies (Shanghai Majorbio)
PRJNA376205	Scaffolds	Lactobacillus	Lactobacillus reuteri and johnsonii Genome sequencing and assembly (Cornell University)
PRJNA392822	Contigs	Lactobacillus	Comparative genomics of Lactobacillus Firm-5 clade (University of Lausanne)
PRJNA578299	Contigs	Lactobacillus	Draft genome sequences of Nono isolates (Max Rubner-Institut)
PRJNA283920	Scaffolds	Lactobacillus acetotolerans	Lactobacillus acetotolerans strain:BM-LA14527 Genome sequencing and assembly (South China University of...)
PRJNA342757	SRA or Trace	Lactobacillus acidophilus	Probiotic trial of Lactobacillus acidophilus (OUCRU Vietnam)
PRJNA227335	Scaffolds	Lactobacillus acidophilus CFH	Lactobacillus acidophilus CFH Genome sequencing and assembly (Los Alamos National Laboratory)
PRJNA257137	Scaffolds	Lactobacillus apis	Lactobacillus apis strain:Hma11 Genome sequencing and assembly (Uppsala university)
PRJNA303235	SRA or Trace	Lactobacillus apis	Lactobacillus apis R-53131 genome sequencing (DOE Joint Genome Institute)
PRJNA303236	SRA or Trace	Lactobacillus bombicola	Lactobacillus sp. R-53102 genome sequencing (DOE Joint Genome Institute)
PRJNA533291	Contigs	Lactobacillus buchneri, Lactobacillus amylovorus, Lactobacillus casei, Lactobacillus curvatus, and Enterococcus hirae genome sequencing and assembly	Lactobacillus buchneri, Lactobacillus amylovorus, Lactobacillus casei, Lactobacillus curvatus, and Enterococcus hirae genome sequencing and assembly (Agriculture and Agri-Food...)
PRJNA436228	SRA or Trace	Lactobacillus casei Genome re-sequencing	Lactobacillus casei Genome re-sequencing (Ministry of Education, Inner...)
PRJNA272101	Scaffolds	Lactobacillus crispatus	HMP reference genome (The Genome Institute at Washington...)
PRJNA557339	Contigs	Lactobacillus crispatus	Lactobacillus crispatus strain:CIP 104459 Genome sequencing and assembly (Rouen University)
PRJNA563077	Scaffolds	Lactobacillus crispatus	Lactobacillus crispatus NCK strains (North Carolina State University)
PRJNA50159	SRA or Trace	Lactobacillus crispatus EX533959VC01	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50163	SRA or Trace	Lactobacillus crispatus EX533959VC03	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50165	SRA or Trace	Lactobacillus crispatus EX533959VC04	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50167	SRA or Trace	Lactobacillus crispatus EX533959VC05	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50169	SRA or Trace	Lactobacillus crispatus EX533959VC06	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50173	SRA or Trace	Lactobacillus crispatus EX533959VC13	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50051	SRA or Trace	Lactobacillus crispatus EX849587VC01	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50053	SRA or Trace	Lactobacillus crispatus EX849587VC02	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50057	SRA or Trace	Lactobacillus crispatus EX849587VC04	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50063	SRA or Trace	Lactobacillus crispatus EX849587VC07	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50067	SRA or Trace	Lactobacillus crispatus EX849587VC08	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA52107	Scaffolds	Lactobacillus crispatus FB049-03	Reference genome for the Human Microbiome Project (Broad Institute)
PRJNA52105	Scaffolds	Lactobacillus crispatus FB077-07	Reference genome for the Human Microbiome Project (Broad Institute)
PRJEB24713	Contigs	Lactobacillus fermentum CECT 9269	Whole genome sequencing of Lactobacillus fermentum CECT 9269 (University of Valencia, Spain)
PRJNA272102	Scaffolds	Lactobacillus gasseri	HMP reference genome (The Genome Institute at Washington...)
PRJNA382771	SRA or Trace	Lactobacillus gasseri	Lactobacillus gasseri Genome sequencing and assembly (*Qingdao Municipal Hospital)
PRJNA84	Complete genome	Lactobacillus gasseri ATCC 33323 = JCM 1131	Major homofermentative Lactobacillus in human intestinal tract (US DOE Joint Genome Institute...)
PRJNA50115	SRA or Trace	Lactobacillus gasseri EX336960VC01	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50117	SRA or Trace	Lactobacillus gasseri EX336960VC02	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50125	SRA or Trace	Lactobacillus gasseri EX336960VC03	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50133	SRA or Trace	Lactobacillus gasseri EX336960VC10	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50139	SRA or Trace	Lactobacillus gasseri EX336960VC13	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50141	SRA or Trace	Lactobacillus gasseri EX336960VC15	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA257138	Scaffolds	Lactobacillus helsingborgensis	Lactobacillus helsingborgensis strain:Bma5 Genome sequencing and assembly (Uppsala university)
PRJNA52121	SRA or Trace	Lactobacillus iners ACS-070-V-Col3	Reference genome for the Human Microbiome Project (Broad Institute)
PRJNA176000	Contigs	Lactobacillus intestinalis	Mouse Model Colitis (Broad Institute)
PRJNA50161	SRA or Trace	Lactobacillus jensenii EX533959VC02	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50055	SRA or Trace	Lactobacillus jensenii EX849587VC03	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50059	SRA or Trace	Lactobacillus jensenii EX849587VC05	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50061	SRA or Trace	Lactobacillus jensenii EX849587VC06	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA315676	SRA or Trace	Lactobacillus johnsonii	Lactobacillus johnsonii Genome sequencing (Pennsylvania State University)
PRJNA257853	SRA or Trace	Lactobacillus kefiranofaciens	Lactobacillus kefiranofaciens strain:ATCC 43761 Genome sequencing (DOE Joint Genome Institute)
PRJNA257141	Scaffolds	Lactobacillus kimbladii	Lactobacillus kimbladii strain:Hma2 Genome sequencing and assembly (Uppsala university)
PRJNA257142	Scaffolds	Lactobacillus kullabergensis	Lactobacillus kullabergensis strain:Biut2 Genome sequencing and assembly (Uppsala university)
PRJNA257139	Scaffolds	Lactobacillus melliventris	Lactobacillus melliventris strain:Hma8 Genome sequencing and assembly (Uppsala university)
PRJDB6495	Complete genome	Lactobacillus paragasseri	Genome project of Lactobacillus paragasseri and related species (National Institure of Genetics)
PRJEB24689	Contigs	Lactobacillus plantarum CECT 8962	Whole genome sequencing of Lactobacillus plantarum CECT 8962 (University of Valencia, Spain)
PRJEB24699	Contigs	Lactobacillus plantarum CECT 8963	Whole genome sequencing of Lactobacillus plantarum CECT 8963 (University of Valencia, Spain)
PRJEB24700	Contigs	Lactobacillus plantarum CECT 8964	Whole genome sequencing of Lactobacillus plantarum CECT 8964 (University of Valencia, Spain)
PRJEB24698	Contigs	Lactobacillus plantarum CECT 8965	Whole genome sequencing of Lactobacillus plantarum CECT 8965 (University of Valencia, Spain)
PRJEB24701	Contigs	Lactobacillus plantarum CECT 8966	Whole genome sequencing of Lactobacillus plantarum CECT 8966 (University of Valencia, Spain)
PRJEB31213	Contigs	Lactobacillus plantarum CECT 9434	Whole genome sequencing of Lactobacillus plantarum CECT 9434, a natural mutant riboflavin overproducer derived from the strain Lactobacillus plantarum CECT 8962 (University of Valencia, Spain)
PRJEB31289	Contigs	Lactobacillus plantarum CECT 9435	Whole genome sequencing of Lactobacillus plantarum CECT 9435, a natural mutant riboflavin overproducer derived from the strain Lactobacillus plantarum CECT 8965 (University of Valencia, Spain)
PRJEB31301	Contigs	Lactobacillus plantarum CECT 9492	Whole genome sequencing of Lactobacillus plantarum CECT 9492 (University of Valencia, Spain)
PRJEB31307	Contigs	Lactobacillus plantarum CECT 9571	Whole genome sequencing of Lactobacillus plantarum CECT 9571, a natural mutant riboflavin overproducer derived from the strain Lactobacillus plantarum CECT 9492 (University of Valencia, Spain)
PRJNA188921	Scaffolds	Lactobacillus psittaci DSM 15354	Lactobacillus psittaci DSM 15354 (DOE Joint Genome Institute)
PRJEB24715	Contigs	Lactobacillus sakei CECT 9267	Whole genome sequencing of Lactobacillus sakei CECT 9267 (University of Valencia, Spain)
PRJEB26638	Contigs	Lactobacillus sakei CECT 9624	Whole genome sequencing of Lactobacillus sakei CECT 9624 (University of Valencia, Spain)
PRJNA300123	Scaffolds	Lactobacillus sp. HMSC056D05	HMP reference genome (The Genome Institute at Washington...)
PRJNA300023	Scaffolds	Lactobacillus sp. HMSC061B07	HMP reference genome (The Genome Institute at Washington...)
PRJNA296274	Scaffolds	Lactobacillus sp. HMSC064F12	HMP reference genome (The Genome Institute at Washington...)
PRJNA299992	Scaffolds	Lactobacillus sp. HMSC066G01	HMP reference genome (The Genome Institute at Washington...)
PRJNA296248	Scaffolds	Lactobacillus sp. HMSC068B07	HMP reference genome (The Genome Institute at Washington...)
PRJNA300015	Scaffolds	Lactobacillus sp. HMSC068F07	HMP reference genome (The Genome Institute at Washington...)
PRJNA296228	Scaffolds	Lactobacillus sp. HMSC072E07	HMP reference genome (The Genome Institute at Washington...)
PRJNA300088	Scaffolds	Lactobacillus sp. HMSC073B09	HMP reference genome (The Genome Institute at Washington...)
PRJNA300179	Scaffolds	Lactobacillus sp. HMSC073D04	HMP reference genome (The Genome Institute at Washington...)
PRJNA300119	Scaffolds	Lactobacillus sp. HMSC075D02	HMP reference genome (The Genome Institute at Washington...)
PRJNA296298	Scaffolds	Lactobacillus sp. HMSC077C11	HMP reference genome (The Genome Institute at Washington...)
PRJNA296309	Scaffolds	Lactobacillus sp. HMSC078F07	HMP reference genome (The Genome Institute at Washington...)
PRJNA269905	Scaffolds	Lactobacillus sp. HMSC08B12	HMP reference genome (The Genome Institute at Washington...)
PRJNA269860	SRA or Trace	Lactobacillus sp. HMSC12B03	HMP reference genome (The Genome Institute at Washington...)
PRJNA269805	Scaffolds	Lactobacillus sp. HMSC17G08	HMP reference genome (The Genome Institute at Washington...)
PRJNA269831	Scaffolds	Lactobacillus sp. HMSC24D01	HMP reference genome (The Genome Institute at Washington...)
PRJNA269832	Scaffolds	Lactobacillus sp. HMSC25A02	HMP reference genome (The Genome Institute at Washington...)
PRJNA554698	Scaffolds	Lactobacillus sp. LL6	Lactobacillus sp. LL6 Genome sequencing and assembly (University of California...)
PRJNA212644	SRA or Trace	Latilactobacillus curvatus F16_9	Human Microbiome Project (HMP) reference genome (Broad Institute)
PRJNA29003	Complete genome	Lentilactobacillus buchneri NRRL B-30929	Isolate with potential for use in biomass conversion (US DOE Joint Genome Institute)
PRJDB4955	Scaffolds	Lentilactobacillus parakefiri	Lactobacillus parakefiri JCM 8573T Genome Sequencing Project (National Agriculture and...)
PRJNA183044	Scaffolds	Levilactobacillus parabrevis ATCC 53295	Levilactobacillus parabrevis ATCC 53295 Genome sequencing and assembly (DOE Joint Genome Institute)
PRJNA533837	Complete genome	Ligilactobacillus animalis	Lactobacillus animalis LL1 genome sequencing and assembly (University of California...)
PRJNA185632	Scaffolds	Ligilactobacillus ceti DSM 22408	Lactobacillus ceti DSM 22408 (DOE Joint Genome Institute)
PRJNA176001	Complete genome	Ligilactobacillus murinus ASF361	Mouse Model Colitis (Broad Institute)
PRJNA322961	SRA or Trace	Ligilactobacillus ruminis	Ligilactobacillus sp. WC1T17 genome sequencing (DOE Joint Genome Institute)
PRJNA254854	SRA or Trace	Ligilactobacillus ruminis DSM 20403 = NBRC 102161	Ligilactobacillus ruminis DSM 20403 = NBRC 102161 Genome sequencing (DOE Joint Genome Institute)
PRJNA185633	Scaffolds	Ligilactobacillus saerimneri DSM 16049	Lactobacillus saerimneri DSM 16049 (DOE Joint Genome Institute)
PRJNA247452	Complete genome	Ligilactobacillus salivarius str. Ren	Ligilactobacillus salivarius str. Ren Genome sequencing (China Agricultural University)
PRJNA312743	Complete genome	Limosilactobacillus fermentum	Genome of L. fermentum 8633 and evolutionary analysis of its probiotic factor, elongation factor Tu. (Universiti Sains Malaysia)
PRJNA347617	Chromosomes	Limosilactobacillus fermentum	Lactobacillus fermentum 47-7 genome sequencing and assembly (Khon Kaen University)
PRJNA476494	Scaffolds	Limosilactobacillus fermentum	Limosilactobacillus fermentum strain:LF2 Genome sequencing and assembly (University College Cork)
PRJDB4156	Contigs	Limosilactobacillus gorillae	Gorilla_Lactic acid bacteria (Animal Science, Graduate...)
PRJNA322958	SRA or Trace	Limosilactobacillus mucosae	Lactobacillus mucosae KHPC15 genome sequencing (DOE Joint Genome Institute)
PRJNA322959	SRA or Trace	Limosilactobacillus mucosae	Lactobacillus mucosae KHPX11 genome sequencing (DOE Joint Genome Institute)
PRJNA322960	SRA or Trace	Limosilactobacillus mucosae	Lactobacillus mucosae WCC8 genome sequencing (DOE Joint Genome Institute)
PRJNA434600	SRA or Trace	Limosilactobacillus reuteri	Limosilactobacillus reuteri Genome sequencing and assembly (University of Wisconsin-Madison)
PRJNA505088	SRA or Trace	Limosilactobacillus reuteri	Lactobacillus reuteri strain LR CGMCC 11154 Raw sequence reads (Guangdong Academy of Agricultural...)
PRJNA554696	Complete genome	Limosilactobacillus reuteri	Limosilactobacillus reuteri strain:LL7 Genome sequencing and assembly (University of California...)
PRJNA298448	SRA or Trace	Limosilactobacillus reuteri subsp. reuteri	Lactobacillus reuteri raw sequence reads (CSIR-Institute of Microbial...)
PRJNA504605	Contigs	Limosilactobacillus vaginalis	Limosilactobacillus vaginalis strain:CBA-L88 (BV2) Genome sequencing and assembly (Universita Cattolica del...)
PRJNA50135	SRA or Trace	Limosilactobacillus vaginalis EX336960VC11	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA50137	SRA or Trace	Limosilactobacillus vaginalis EX336960VC12	Demonstration Project Reference Genome for Human Microbiome Project (Virginia Commonwealth University)
PRJNA235015	SRA or Trace	Liquorilactobacillus nagelii DSM 13675	Liquorilactobacillus nagelii DSM 13675 Genome sequencing (DOE Joint Genome Institute)
PRJNA336518	Scaffolds	Live Microbial Ingredients Survey	Live Microbial Ingredients Survey (USFDA)
PRJNA481120	SRA or Trace	Mouse microbiota single cell genomes	Mouse microbiota single cell genomes (Gladstone Institutes)
PRJDB1726	Complete genome	Paucilactobacillus hokkaidonensis	Lactobacillus hokkaidonensis LOOC260 Genome Sequence Project (National Agriculture and...)
PRJNA530250	Contigs	Probiotics and Antimicrobial-Resistant Bacteria	Probiotics and Antimicrobial-Resistant Bacteria (Colorado State University)
PRJNA388578	Scaffolds	Probiotics and starter cultures – surface proteins and bacteriocins	Probiotics and starter cultures – surface proteins and bacteriocins (IGA Technology Services Srl)
PRJNA504734	Scaffolds	Safety evaluation of lactic acids bacteria as a potential probiotic	Safety evaluation of lactic acids bacteria as a potential probiotic (North-west University)
PRJNA296754	Scaffolds	Schleiferilactobacillus harbinensis	Schleiferilactobacillus harbinensis strain:BM-LH14723 Genome sequencing and assembly (South China University of...)
PRJNA309616	Scaffolds	Schleiferilactobacillus harbinensis	Schleiferilactobacillus harbinensis strain:BM-LB13908 Genome sequencing and assembly (South China University of...)
PRJNA552757	Complete genome	Schleiferilactobacillus harbinensis	Schleiferilactobacillus harbinensis strain:NSMJ42 Genome sequencing (Nakdonggang National Institute...)
PRJNA188920	Scaffolds	Schleiferilactobacillus harbinensis DSM 16991	Lactobacillus harbinensis DSM 16991 (DOE Joint Genome Institute)
PRJNA573690	Contigs	Sequencing ESKAPE pathogens and Clostridium difficile under different scenarios	Sequencing ESKAPE pathogens and Clostridium difficile under different scenarios (Signature Science, LLC)
PRJNA477598	Chromosomes	Single-molecule detection of N6-methyladenine in microbial reference materials	Single-molecule detection of N6-methyladenine in microbial reference materials (Weill Cornell Medicine)
PRJEB10572	Chromosomes	The cultivable fraction of mouse gut	The mouse intestinal bacterial collection (miBC) represents a unique resource of cultivable bacteria isolates from mice that enables engineering of minimal gut consortia. (Technical University Munich)
PRJEB14693	Contigs	Whole Genome Sequencing of three Lactobacillus plantarum probiotic strains isolated from dairy products	Illumina Miseq genome sequencing of three Lactobacillus plantarum strains isolated from dairy products by CREA-FLC(Italy) (Istituto Zooprofilattico...)
PRJNA377666	Contigs	Whole genome sequencing of chicken gut anaerobes	Whole genome sequencing of chicken gut anaerobes (Veterinary Research Institute)
PRJNA257876	SRA or Trace	[Lactobacillus] rogosae	[Lactobacillus] rogosae strain:ATCC 27753 Genome sequencing (DOE Joint Genome Institute)
PRJNA289613	Chromosomes	mouse gut metagenome	Genome sequencing and assembly of a defined mouse intestinal bacterial community (Max von Pettenkofer-Institut)

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Other

BioProject accession	Name	Title
PRJEB18589	Commensal_bacterial_genomes_from_health_and_disease	Commensal_bacterial_genomes_from_health_and_disease (Wellcome Sanger Institute)
PRJEB21680	Drakenstein12internal	Drakenstein12internal (Wellcome Sanger Institute)
PRJEB22112	Extensive culturing of bladder bacteria reveals a highly connected urogenital microbiome	Bladder culture collection reveals interconnected urogenital microbiome (WELLCOME TRUST SANGER INSTITUTE)
PRJEB2824	Generation_of_draft_genomes_for_supershedder_and_bacteriotherapy_bacteria	Generation_of_draft_genomes_for_supershedder_and_bacteriotherapy_bacteria (Wellcome Sanger Institute)
PRJEB29398	Genome sequencing: Raw data of Lactobacillus plantarum CRL 681	Genome sequencing: Raw data of Lactobacillus plantarum CRL 681 (CERELA)

List all 17 'Other' projects...

BioProject accession	Name	Title
PRJEB18589	Commensal_bacterial_genomes_from_health_and_disease	Commensal_bacterial_genomes_from_health_and_disease (Wellcome Sanger Institute)
PRJEB21680	Drakenstein12internal	Drakenstein12internal (Wellcome Sanger Institute)
PRJEB22112	Extensive culturing of bladder bacteria reveals a highly connected urogenital microbiome	Bladder culture collection reveals interconnected urogenital microbiome (WELLCOME TRUST SANGER INSTITUTE)
PRJEB2824	Generation_of_draft_genomes_for_supershedder_and_bacteriotherapy_bacteria	Generation_of_draft_genomes_for_supershedder_and_bacteriotherapy_bacteria (Wellcome Sanger Institute)
PRJEB29398	Genome sequencing: Raw data of Lactobacillus plantarum CRL 681	Genome sequencing: Raw data of Lactobacillus plantarum CRL 681 (CERELA)
PRJEB23845	Genomic_and_bacterial_blueprint_of_the_human_gastrointestinal_microbiota	Genomic_and_bacterial_blueprint_of_the_human_gastrointestinal_microbiota (Wellcome Sanger Institute)
PRJEB8104	Genomic_characterization_of_bladder_bacteria_from_healthy_and_infected_women	Genomic_characterization_of_bladder_bacteria_from_healthy_and_infected_women (Wellcome Sanger Institute)
PRJEB2977	Identification_of_mutational_spectra_in_fission_yeast_DNA_repair_and_chromatin_mutants__S_cerevisiae_	Identification_of_mutational_spectra_in_fission_yeast_DNA_repair_and_chromatin_mutants__S_cerevisiae_ (Wellcome Sanger Institute)
PRJEB11980	Lactobacillus plantarum	WGS of Lactobacillus plantarum isolated from human gut (JUSTUS LIEBIG UNIVERSITY)
PRJEB5094	Lactobacillus sequencing project	Whole genome sequencing of isolates from Lactobacillus acidophilus and closely related organisms (University of Oxford)
PRJEB3060	Lactobacillus_in_severe_early_childhood_caries	Lactobacillus_in_severe_early_childhood_caries (Wellcome Sanger Institute)
PRJEB2631	MetaHIT_single_cell	MetaHIT_single_cell (Wellcome Sanger Institute)
PRJEB9718	Microbiome proliferation	Growth dynamics of gut microbiota in health and disease inferred from single metagenomic samples (WEIZMANN INSTITUE OF SCIENCE)
PRJNA224116	Refseq Prokaryotic Genome Annotation Project	Refseq Prokaryotic Genome Annotation Project (NCBI)
PRJEB25194	SGV - Microbiome	Sub-genomic variation in the gut microbiome associates with host metabolic health (WEIZMANN INSTITUE OF SCIENCE)
PRJEB19875	Sequencing human gut bacteria	Genomes of a representative collection of cultivable human gut bacteria to decipher metabolic capacities of individual species (EMBL EUROPEAN BIOINFORMATICS...)
PRJEB29504	Ultra-deep, long-read nanopore sequencing of mock microbial community standards	Ultra-deep, long-read nanopore sequencing of mock microbial community standards (University of Birmingham,...)

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Phenotype or Genotype

BioProject accession	Organism	Title
PRJDB5065	Bacteria	Pig lactic acid bacteria (Animal Science, Graduate...)

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The Lactobacillus genus, a use case for Bactopia.

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