MyMedR

Complete genome sequence of Novosphingobium resinovorum SA1, a versatile xenobiotic-degrading bacterium capable of utilizing sulfanilic acid

Hegedűs B, Kós PB, Bálint B, Maróti G, Gan HM, Perei K, et al.

J Biotechnol, 2017 Jan 10;241:76-80.

PMID: 27851894 DOI: 10.1016/j.jbiotec.2016.11.013

Sulfanilic acid (4-aminobenzenesulfonic acid) is a sulfonated aromatic amine widely used in chemical industries for synthesis of various organic dyes and sulfa drugs. There are quite a few microbial co-cultures or single isolates capable of completely degrading this compound. Novosphingobium resinovorum SA1 was the first single bacterium which could utilize sulfanilic acid as its sole carbon, nitrogen and sulfur source. The strain has versatile catabolic routes for the bioconversion of numerous other aromatic compounds. Here, the complete genome sequence of the N. resinovorum SA1 strain is reported. The genome consists of a circular chromosome of 3.8 Mbp and four extrachromosomal elements between 67 and 1 759.8 kbp in size. Three alternative 3-ketoadipate pathways were identified on the plasmids. Sulfanilic acid is decomposed via a modified 3-ketoadipate pathway and the oxygenases involved form a phylogenetically separate branch on the tree. Sequence analysis of these elements might provide a genetic background for deeper insight into the versatile catabolic metabolism of various aromatic xenobiotics, including sulfanilic acid and its derivatives. Moreover, this is also a good model strain for understanding the role and evolution of multiple genetic elements within a single strain.

Crustal fluid and ash alteration impacts on the biosphere of Shikoku Basin sediments, Nankai Trough, Japan

Torres ME, Cox T, Hong WL, McManus J, Sample JC, Destrigneville C, et al.

Geobiology, 2015 Nov;13(6):562-80.

PMID: 26081483 DOI: 10.1111/gbi.12146

We present data from sediment cores collected from IODP Site C0012 in the Shikoku Basin. Our site lies at the Nankai Trough, just prior to subduction of the 19 Ma Philippine Sea plate. Our data indicate that the sedimentary package is undergoing multiple routes of electron transport and that these differing pathways for oxidant supply generate a complex array of metabolic routes and microbial communities involved in carbon cycling. Numerical simulations matched to pore water data document that Ca(2+) and Cl(1-) are largely supplied via diffusion from a high-salinity (44.5 psu) basement fluid, which supports the presence of halophile Archean communities within the deep sedimentary package that are not observed in shallow sediments. Sulfate supply from basement supports anaerobic oxidation of methane (AOM) at a rate of ~0.2 pmol cm(-3) day(-1) at ~400 mbsf. We also note the disappearance of δ-Proteobacteria at 434 mbsf, coincident with the maximum in methane concentration, and their reappearance at 463 mbsf, coinciding with the observed deeper increase in sulfate concentration toward the basement. We did not, however, find ANME representatives in any of the samples analyzed (from 340 to 463 mbsf). The lack of ANME may be due to an overshadowing effect from the more dominant archaeal phylotypes or may indicate involvement of unknown groups of archaea in AOM (i.e., unclassified Euryarchaeota). In addition to the supply of sulfate from a basement aquifer, the deep biosphere at this site is also influenced by an elevated supply of reactive iron (up to 143 μmol g(-1)) and manganese (up to 20 μmol g(-1)). The effect of these metal oxides on the sulfur cycle is inferred from an accompanying sulfur isotope fractionation much smaller than expected from traditional sulfate-reducing pathways. The detection of the manganese- and iron-reducer γ-Proteobacteria Alteromonas at 367 mbsf is consistent with these geochemical inferences.

DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

Brandon-Mong GJ, Gan HM, Sing KW, Lee PS, Lim PE, Wilson JJ

Bull. Entomol. Res., 2015 Dec;105(6):717-27.

PMID: 26344799 DOI: 10.1017/S0007485315000681

Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80-90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.

Fulltext Data on whole-genome sequencing of extended-spectrum beta-lactamases producing Enterobacteriaceae isolates from Malaysia

Gan HM, Eng WWH, Dhanoa A

Data Brief, 2019 Aug;25:104257.

PMID: 31384648 DOI: 10.1016/j.dib.2019.104257

We report the whole genome sequencing data and de novo genome assemblies for eight extended-spectrum beta-lactamases (ESBL) producing Enterobacteriaceae isolates from Malaysia consisting of four Klebsiella pneumoniae, two Enterobacter harmaechei, one Citrobacter freundii and one Escherichia coli. We identified at least one ESBL gene in each genome, with blaCTX-M-15 being the most prevalent ESBL gene in the current genomic sampling.

Fulltext De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read

Austin CM, Tan MH, Harrisson KA, Lee YP, Croft LJ, Sunnucks P, et al.

Gigascience, 2017 08 01;6(8):1-6.

PMID: 28873963 DOI: 10.1093/gigascience/gix063

One of the most iconic Australian fish is the Murray cod, Maccullochella peelii (Mitchell 1838), a freshwater species that can grow to ∼1.8 metres in length and live to age ≥48 years. The Murray cod is of a conservation concern as a result of strong population contractions, but it is also popular for recreational fishing and is of growing aquaculture interest. In this study, we report the whole genome sequence of the Murray cod to support ongoing population genetics, conservation, and management research, as well as to better understand the evolutionary ecology and history of the species. A draft Murray cod genome of 633 Mbp (N50 = 109 974bp; BUSCO and CEGMA completeness of 94.2% and 91.9%, respectively) with an estimated 148 Mbp of putative repetitive sequences was assembled from the combined sequencing data of 2 fish individuals with an identical maternal lineage; 47.2 Gb of Illumina HiSeq data and 804 Mb of Nanopore data were generated from the first individual while 23.2 Gb of Illumina MiSeq data were generated from the second individual. The inclusion of Nanopore reads for scaffolding followed by subsequent gap-closing using Illumina data led to a 29% reduction in the number of scaffolds and a 55% and 54% increase in the scaffold and contig N50, respectively. We also report the first transcriptome of Murray cod that was subsequently used to annotate the Murray cod genome, leading to the identification of 26 539 protein-coding genes. We present the whole genome of the Murray cod and anticipate this will be a catalyst for a range of genetic, genomic, and phylogenetic studies of the Murray cod and more generally other fish species of the Percichthydae family.

Fulltext Deciphering chicken gut microbial dynamics based on high-throughput 16S rRNA metagenomics analyses

Mohd Shaufi MA, Sieo CC, Chong CW, Gan HM, Ho YW

Gut Pathog, 2015;7:4.

PMID: 25806087 DOI: 10.1186/s13099-015-0051-7

Chicken gut microbiota has paramount roles in host performance, health and immunity. Understanding the topological difference in gut microbial community composition is crucial to provide knowledge on the functions of each members of microbiota to the physiological maintenance of the host. The gut microbiota profiling of the chicken was commonly performed previously using culture-dependent and early culture-independent methods which had limited coverage and accuracy. Advances in technology based on next-generation sequencing (NGS), offers unparalleled coverage and depth in determining microbial gut dynamics. Thus, the aim of this study was to investigate the ileal and caecal microbiota development as chicken aged, which is important for future effective gut modulation.

Fulltext Digging deeper: new gene order rearrangements and distinct patterns of codons usage in mitochondrial genomes among shrimps from the Axiidea, Gebiidea and Caridea (Crustacea: Decapoda)

Tan MH, Gan HM, Lee YP, Poore GC, Austin CM

PeerJ, 2017;5:e2982.

PMID: 28265498 DOI: 10.7717/peerj.2982

BACKGROUND: Whole mitochondrial DNA is being increasingly utilized for comparative genomic and phylogenetic studies at deep and shallow evolutionary levels for a range of taxonomic groups. Although mitogenome sequences are deposited at an increasing rate into public databases, their taxonomic representation is unequal across major taxonomic groups. In the case of decapod crustaceans, several infraorders, including Axiidea (ghost shrimps, sponge shrimps, and mud lobsters) and Caridea (true shrimps) are still under-represented, limiting comprehensive phylogenetic studies that utilize mitogenomic information.

METHODS: Sequence reads from partial genome scans were generated using the Illumina MiSeq platform and mitogenome sequences were assembled from these low coverage reads. In addition to examining phylogenetic relationships within the three infraorders, Axiidea, Gebiidea, and Caridea, we also investigated the diversity and frequency of codon usage bias and mitogenome gene order rearrangements.

RESULTS: We present new mitogenome sequences for five shrimp species from Australia that includes two ghost shrimps, Callianassa ceramica and Trypaea australiensis, along with three caridean shrimps, Macrobrachium bullatum, Alpheus lobidens, and Caridina cf. nilotica. Strong differences in codon usage were discovered among the three infraorders and significant gene order rearrangements were observed. While the gene order rearrangements are congruent with the inferred phylogenetic relationships and consistent with taxonomic classification, they are unevenly distributed within and among the three infraorders.

DISCUSSION: Our findings suggest potential for mitogenome rearrangements to be useful phylogenetic markers for decapod crustaceans and at the same time raise important questions concerning the drivers of mitogenome evolution in different decapod crustacean lineages.

Fulltext Draft Genome Sequence of Clostridium bifermentans Strain WYM, a Promising Biohydrogen Producer Isolated from Landfill Leachate Sludge

Wong YM, Juan JC, Gan HM, Austin CM

Genome Announc, 2014;2(2).

PMID: 24604639 DOI: 10.1128/genomeA.00077-14

Clostridium bifermentans strain WYM is an effective biohydrogen producer isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the metabolic pathways involved in efficient biohydrogen production.

Fulltext Draft Genome Sequence of Clostridium perfringens Strain JJC, a Highly Efficient Hydrogen Producer Isolated from Landfill Leachate Sludge

Wong YM, Juan JC, Gan HM, Austin CM

Genome Announc, 2014;2(2).

PMID: 24604637 DOI: 10.1128/genomeA.00064-14

Clostridium perfringens strain JJC is an effective biohydrogen and biochemical producer that was isolated from landfill leachate sludge. Here, we present the assembly and annotation of its genome, which may provide further insights into the gene interactions involved in efficient biohydrogen production.

Fulltext Draft Genome Sequence of Clostridium sp. Strain Ade.TY, a New Biohydrogen- and Biochemical-Producing Bacterium Isolated from Landfill Leachate Sludge

Wong YM, Juan JC, Ting A, Wu TY, Gan HM, Austin CM

Genome Announc, 2014;2(2).

PMID: 24604640 DOI: 10.1128/genomeA.00078-14

Clostridium sp. strain Ade.TY is potentially a new biohydrogen-producing species isolated from landfill leachate sludge. Here we present the assembly and annotation of its genome, which may provide further insights into its gene interactions for efficient biohydrogen production.

Fulltext Draft Genome Sequence of Jeotgalibacillus soli DSM 23228, a Bacterium Isolated from Alkaline Sandy Soil

Goh KM, Chan KG, Yaakop AS, Chan CS, Ee R, Tan WS, et al.

Genome Announc, 2015;3(3).

PMID: 25999554 DOI: 10.1128/genomeA.00512-15

Jeotgalibacillus soli, a bacterium capable of degrading N-acyl homoserine lactone, was isolated from a soil sample in Portugal. J. soli constitutes the only Jeotgalibacillus species isolated from a non-marine source. Here, the draft genome, several interesting glycosyl hydrolases, and its putative N-acyl homoserine lactonases are presented.

Fulltext Draft Genome Sequence of Paenibacillus sp. Strain MSt1 with Broad Antimicrobial Activity, Isolated from Malaysian Tropical Peat Swamp Soil

Aw YK, Ong KS, Yule CM, Gan HM, Lee SM

Genome Announc, 2014;2(5).

PMID: 25301658 DOI: 10.1128/genomeA.01024-14

We report the draft genome sequence of Paenibacillus sp. strain MSt1, which has broad-range antimicrobial activity, isolated from tropical peat swamp soil. Genes involved in antimicrobial biosynthesis are found to be present in this genome.

Fulltext Draft Genome Sequence of Yellow Pigmented Jeotgalibacillus alimentarius JY-13T, the First Halophile Strain of the Genus Jeotgalibacillus

Yaakop AS, Chan KG, Gan HM, Goh KM

Genome Announc, 2015;3(5).

PMID: 26494670 DOI: 10.1128/genomeA.01224-15

Jeotgalibacillus alimentarius JY-13(T) (=KCCM 80002(T) = JCM 10872(T)) is a moderate halophile. In 2001, this was the first strain of the newly proposed Jeotgalibacillus genus. The draft genome of J. alimentarius was found to consist of 32 contigs (N50, 315,125 bp) with a total size of 3,364,745 bp. This genome information will be helpful for studies on pigmentation as well as applications for this bacterium.

Fulltext Draft Genome Sequences of Six Enterococcus faecalis Strains Isolated from Malaysian Clinical and Environmental Origins

Daniel DS, Gan HM, Lee SM, Dykes GA, Rahman S

Genome Announc, 2017 Jun 15;5(24).

PMID: 28619812 DOI: 10.1128/genomeA.00553-17

Enterococcus faecalis is known to cause a variety of nosocomial infections, including urinary tract infections. Antibiotic resistance and virulence properties in this species are of public concern. The draft genome sequences of six E. faecalis strains isolated from clinical and environmental sources in Malaysia are presented here.

Fulltext Draft Genome Sequences of Two Antimicrobial-Producing Burkholderia sp. Strains, MSh1 and MSh2, Isolated from Malaysian Tropical Peat Swamp Forest Soil

Ong KS, Aw YK, Gan HM, Yule CM, Lee SM

Genome Announc, 2014;2(5).

PMID: 25301661 DOI: 10.1128/genomeA.01032-14

We report the draft genome sequences of two antimicrobial-producing isolates, Burkholderia sp. strains MSh1 and MSh2, which were isolated from tropical peat swamp forest soil. Putative genes related to different antimicrobial production have been annotated in both genome sequences.

Fulltext Draft Genome Sequences of Two Cellulolytic Paenibacillus sp. Strains, MAEPY1 and MAEPY2, from Malaysian Landfill Leachate

Chua P, Yoo HS, Gan HM, Lee SM

Genome Announc, 2014;2(1).

PMID: 24526641 DOI: 10.1128/genomeA.00065-14

We report the draft genome sequences of two Paenibacillus species with cellulose-degrading abilities isolated from landfill leachate. An array of genes putatively involved in cellulose degradation have been identified in both genome sequences, which can benefit various biotechnological industries.

Draft genome of Jeotgalibacillus campisalis SF-57(T), a moderate halophilic bacterium isolated from marine saltern

Yaakop AS, Chan KG, Gan HM, Goh KM

Mar Genomics, 2015 Oct;23:59-60.

PMID: 25999308 DOI: 10.1016/j.margen.2015.05.004

Jeotgalibacillus campisalis SF-57(T) (=KCCM 41644(T), JCM 11810(T)) is a moderate halophilic bacterium isolated from a Korean marine saltern. In this study, we describe the high-quality draft genome of strain SF-57(T), which was assembled into 24 contigs containing 3,650,490bp with a G+C content of 41.06%. Availability of the genome sequence of J. campisalis SF-57(T) will contribute to a better understanding of the genus Jeotgalibacillus.

Fulltext Draft genome sequence of Pantoea sp. strain A4, a Rafflesia-associated bacterium that produces N-acylhomoserine lactones as quorum-sensing molecules

Hong KW, Gan HM, Low SM, Lee PK, Chong YM, Yin WF, et al.

J Bacteriol, 2012 Dec;194(23):6610.

PMID: 23144374 DOI: 10.1128/JB.01619-12

Pantoea sp. strain A4 is a Gram-negative bacterium isolated from the Rafflesia flower. We present here, for the first time, the genome sequence of Rafflesia-associated Pantoea sp. strain A4, which exhibited quorum-sensing activity.

Fulltext Dumpster diving for diatom plastid 16S rRNA genes

Bonfantine KL, Trevathan-Tackett SM, Matthews TG, Neckovic A, Gan HM

PeerJ, 2021;9:e11576.

PMID: 34249491 DOI: 10.7717/peerj.11576

High throughput sequencing is improving the efficiency of monitoring diatoms, which inhabit and support aquatic ecosystems across the globe. In this study, we explored the potential of a standard V4 515F-806RB primer pair in recovering diatom plastid 16S rRNA sequences. We used PhytoREF to classify the 16S reads from our freshwater biofilm field sampling from three stream segments across two streams in south-eastern Australia and retrieved diatom community data from other, publicly deposited, Australian 16S amplicon datasets. When these diatom operational taxonomic units (OTUs) were traced using the default RDPII and NCBI databases, 68% were characterized as uncultured cyanobacteria. We analysed the 16S rRNA sequences from 72 stream biofilm samples, separated the chloroplast OTUs, and classified them using the PhytoREF database. After filtering the reads attributed to Bacillariophyta (relative abundance >1%), 71 diatom OTUs comprising more than 90% of the diatom reads in each stream biofilm sample were identified. Beta-diversity analyses demonstrated significantly different diatom assemblages and discrimination among river segments. To further test the approach, the diatom OTUs from our biofilm sampling were used as reference sequences to identify diatom reads from other Australian 16S rRNA datasets in the NCBI-SRA database. Across the three selected public datasets, 67 of our 71 diatom OTUs were detected in other Australian ecosystems. Our results show that diatom plastid 16S rRNA genes are readily amplified with existing 515F-806RB primer sets. Therefore, the volume of existing 16S rRNA amplicon datasets initially generated for microbial community profiling can also be used to detect, characterize, and map diatom distribution to inform phylogeny and ecological health assessments, and can be extended into a range of ecological and industrial applications. To our knowledge, this study represents the first attempt to classify freshwater samples using this approach and the first application of PhytoREF in Australia.

Effects of supplementing freeze-dried Mitsuokella jalaludinii phytase on the growth performance and gut microbial diversity of broiler chickens

Tang HC, Sieo CC, Abdullah N, Chong CW, Gan HM, Mohd Asrore MS, et al.

J Anim Physiol Anim Nutr (Berl), 2020 Jan;104(1):116-125.

PMID: 31556187 DOI: 10.1111/jpn.13208

Inclusion of phytase in animal feedstuff is a common practice to enhance nutrients availability. However, little is known about the effects of phytase supplementation on the microbial ecology of the gastrointestinal tract. In this study, freeze-dried Mitsuokella jalaludinii phytase (MJ) was evaluated in a feeding trial with broilers fed a low available phosphorus (aP) diet. A total of 180 male broiler chicks (day-old Cobb) were assigned into three dietary treatments: Control fed with 0.4% (w/w) of available phosphorus (aP); Group T1 fed low aP [0.2% (w/w)] supplemented with MJ; and T2 fed low aP and deactivated MJ. The source of readily available P, dicalcium phosphate (DCP), was removed from low aP diet, whereby additional limestone was provided to replace the amount of Ca normally found in DCP. For each treatment, 4 replicate pens were used, where each pen consisted of 15 animals. The animals' energy intake and caecal bacterial community were monitored weekly for up to 3 weeks. The apparent metabolizable energy (AME) and apparent digestibility of dry matter (ADDM) of broilers fed with different diets were determined. In addition, the caecal microbial diversities of broilers were assessed using high-throughput next-generation sequencing targeting the V3-V4 region of bacterial 16S rRNA. The results showed that broilers fed with T1 diet have better feed conversion ratio (FCR) when compared to the Control (p

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