Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2

Olmos, Alejandro; Henríquez-Piskulich, Patricia; Sánchez, Carolina; Rojas-Herrera, Marcelo; Moreno-Pino, Mario; Gomez, Marcela; Silva, Rafael Rodríguez Da; Maracaja-Coutinho, Vinícius; Aldea, Patricia; Trombert, Annette N.

doi:10.1128/genomea.01013-14

Cited by 6 publications

(17 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The L. kunkeei strain MP2 reported in this study was isolated in a previous study from the gut of a honey bee (Apis mellifera), collected from commune hives in the Maria Pinto area, Melipilla Province in the Central zone of Chile (Olmos et al, 2014).…”

Section: Dna Isolation and Genome Sequencingmentioning

confidence: 86%

“…A comparison of the assembly of L. kunkeei MP2 obtained in this work, with the previously obtained using Illumina sequencing (Olmos et al, 2014), is shown on Figure 1. All of the previous assembled contigs mapped to the current assembly, and several gaps on the sequence were completed in this new version of the genome.…”

Section: Assembly Descriptionmentioning

confidence: 94%

“…Polishing was done using Quiver, using SMRT Analysis version 2.3. Comparisons between the previously sequenced L. kunkeei MP2 genome (Accession number PRJNA257367) (Olmos et al, 2014), as well with the other two available genome sequences (Porcellato et al, 2015;Djukic et al, 2015) were performed using MUMMER (Kurtz et al, 2004). Genome annotation was performed using Prokka version 1.11 (Seemann, 2014).…”

Section: Genome Assembly and Annotationmentioning

confidence: 99%

“…Functional annotation was done using EggNOG V 4.1 (Powell et al, 2014), and the summary of functional categories is shown on Manuscript to be reviewed the chromosome, something that was not possible in the previous sequenced genome of this strain (Olmos et al, 2014).…”

Section: Assembly Descriptionmentioning

confidence: 99%

“…In previous work, we isolated a L. kunkeei strain (named as MP2) from the gut of Chilean honey bees from María Pinto, Melipilla (Olmos et al, 2014). The genome of this strain was sequenced using the Illumina MiSeq platform, which resulted in a draft genome of 44 contigs, for a total genome size of 1,581,395 bp, and 826 well-annotated protein coding-genes (Olmos et al, 2014). The nature of the short-reads used for this assembly, did not allow to completely resolve the genome without gaps.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Peer Review #1 of "Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate (v0.2)"

2016

View full text Add to dashboard Cite

Background. Honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD or Colony Collapsed Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule realtime sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L. kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different

show abstract

Section: Dna Isolation and Genome Sequencingmentioning

confidence: 86%

Section: Assembly Descriptionmentioning

confidence: 94%

Section: Genome Assembly and Annotationmentioning

confidence: 99%

Section: Assembly Descriptionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Peer Review #1 of "Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate (v0.2)"

2016

View full text Add to dashboard Cite

show abstract

Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut

et al. 2015

View full text Add to dashboard Cite

show abstract

BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

Daisley

Reid

2021

mSystems

View full text Add to dashboard Cite

High-throughput 16S rRNA gene sequencing technologies have robust potential to improve our understanding of bee (Hymenoptera: Apoidea)-associated microbial communities and their impact on hive health and disease. Despite recent computation algorithms now permitting exact inferencing of high-resolution exact amplicon sequence variants (ASVs), the taxonomic classification of these ASVs remains a challenge due to inadequate reference databases. To address this, we assemble a comprehensive data set of all publicly available bee-associated 16S rRNA gene sequences, systematically annotate poorly resolved identities via inclusion of 618 placeholder labels for uncultivated microbial dark matter, and correct for phylogenetic inconsistencies using a complementary set of distance-based and maximum likelihood correction strategies. To benchmark the resultant database (BEExact), we compare performance against all existing reference databases in silico using a variety of classifier algorithms to produce probabilistic confidence scores. We also validate realistic classification rates on an independent set of ∼234 million short-read sequences derived from 32 studies encompassing 50 different bee types (36 eusocial and 14 solitary). Species-level classification rates on short-read ASVs range from 80 to 90% using BEExact (with ∼20% due to “bxid” placeholder names), whereas only ∼30% at best can be resolved with current universal databases. A series of data-driven recommendations are developed for future studies. We conclude that BEExact (https://github.com/bdaisley/BEExact) enables accurate and standardized microbiota profiling across a broad range of bee species—two factors of key importance to reproducibility and meaningful knowledge exchange within the scientific community that together, can enhance the overall utility and ecological relevance of routine 16S rRNA gene-based sequencing endeavors. IMPORTANCE The failure of current universal taxonomic databases to support the rapidly expanding field of bee microbiota research has led to many investigators relying on “in-house” reference sets or manual classification of sequence reads (usually based on BLAST searches), often with vague identity thresholds and subjective taxonomy choices. This time-consuming, error- and bias-prone process lacks standardization, cripples the potential for comparative cross-study analysis, and in many cases is likely to incorrectly sway study conclusions. BEExact is structured on and leverages several complementary bioinformatic techniques to enable refined inference of bee host-associated microbial communities without any other methodological modifications necessary. It also bridges the gap between current practical outcomes (i.e., phylotype-to-genus level constraints with 97% operational taxonomic units [OTUs]) and the theoretical resolution (i.e., species-to-strain level classification with 100% ASVs) attainable in future microbiota investigations. Other niche habitats could also likely benefit from customized database curation via implementation of the novel approaches introduced in this study.

show abstract

Draft Genome of Chilean Honeybee (Apis mellifera) Gut Strain Lactobacillus kunkeei MP2

Abstract: Here, we report the first draft genome sequence of Lactobacillus kunkeei strain MP2, isolated from a Chilean honeybee gut. The sequenced genome has a total size of 1.58 Mb distributed into 44 contigs and 1,356 protein-coding sequences.

Cited by 6 publications

References 11 publications

Peer Review #1 of "Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate (v0.2)"

Peer Review #1 of "Genome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate (v0.2)"

Draft Genome Sequence of Lactobacillus kunkeei AR114 Isolated from Honey Bee Gut

BEExact: a Metataxonomic Database Tool for High-Resolution Inference of Bee-Associated Microbial Communities

Contact Info

Product

Resources

About