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Modulatory effects of condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid on the bovine rumen bacterial community in vitro

Saminathan M, Sieo CC, Gan HM, Ravi S, Venkatachalam K, Abdullah N, et al.

J Sci Food Agric, 2016 Oct;96(13):4565-74.
PMID: 26910767 DOI: 10.1002/jsfa.7674

BACKGROUND: Condensed tannin (CT) fractions of different molecular weights (MWs) may affect rumen microbial metabolism by altering bacterial diversity. In this study the effects of unfractionated CTs (F0) and five CT fractions (F1-F5) of different MWs (F1, 1265.8 Da; F2, 1028.6 Da; F3, 652.2 Da; F4, 562.2 Da; F5, 469.6 Da) from Leucaena leucocephala hybrid-Rendang (LLR) on the structure and diversity of the rumen bacterial community were investigated in vitro.
RESULTS: Real-time polymerase chain reaction assay showed that the total bacterial population was not significantly (P > 0.05) different among the dietary treatments. Inclusion of higher-MW CT fractions F1 and F2 significantly (P
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.
Fulltext Isolation, Identification, Whole-Genome Sequencing, and Annotation of Four Bacillus Species, B. anthracis RIT375, B. circulans RIT379, B. altitudinis RIT380, and B. megaterium RIT381, from Internal Stem Tissue of the Insulin Plant Costus igneus

Polter SJ, Caraballo AA, Lee YP, Eng WW, Gan HM, Wheatley MS, et al.

Genome Announc, 2015;3(4).
PMID: 26227604 DOI: 10.1128/genomeA.00847-15

Here, we report the isolation, identification, whole-genome sequencing, and annotation of four Bacillus species from internal stem tissue of the insulin plant Costus igneus, grown in Puerto Rico. The plant is of medicinal importance, as extracts from its leaves have been shown to lower blood sugar levels of hyperglycemic rats.
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 Metabolomics and 16S rRNA sequencing of human colorectal cancers and adjacent mucosa

Loke MF, Chua EG, Gan HM, Thulasi K, Wanyiri JW, Thevambiga I, et al.

PLoS One, 2018;13(12):e0208584.
PMID: 30576312 DOI: 10.1371/journal.pone.0208584

Colorectal cancer (CRC) is ranked the third most common cancer in human worldwide. However, the exact mechanisms of CRC are not well established. Furthermore, there may be differences between mechanisms of CRC in the Asian and in the Western populations. In the present study, we utilized a liquid chromatography-mass spectrometry (LC-MS) metabolomic approach supported by the 16S rRNA next-generation sequencing to investigate the functional and taxonomical differences between paired tumor and unaffected (normal) surgical biopsy tissues from 17 Malaysian patients. Metabolomic differences associated with steroid biosynthesis, terpenoid biosynthesis and bile metabolism could be attributed to microbiome differences between normal and tumor sites. The relative abundances of Anaerotruncus, Intestinimonas and Oscillibacter displayed significant relationships with both steroid biosynthesis and terpenoid and triterpenoid biosynthesis pathways. Metabolites involved in serotonergic synapse/ tryptophan metabolism (Serotonin and 5-Hydroxy-3-indoleacetic acid [5-HIAA]) were only detected in normal tissue samples. On the other hand, S-Adenosyl-L-homocysteine (SAH), a metabolite involves in methionine metabolism and methylation, was frequently increased in tumor relative to normal tissues. In conclusion, this study suggests that local microbiome dysbiosis may contribute to functional changes at the cancer sites. Results from the current study also contributed to the list of metabolites that are found to differ between normal and tumor sites in CRC and supported our quest for understanding the mechanisms of carcinogenesis.
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
Fulltext The complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) from Peninsular Malaysia

Rosli N, Sitam FT, Rovie-Ryan JJ, Gan HM, Lee YP, Hartini Ithnin, et al.

Mitochondrial DNA B Resour, 2019 Jul 13;4(2):2535-2536.
PMID: 33365614 DOI: 10.1080/23802359.2019.1640085

Here, we present the first complete mitochondrial genome of Malayan Gaur (Bos gaurus hubbacki) inferred using next-generation sequencing. The mitogenome is 16,367 bp in length with the structural organization of a typical bovine mitochondrial arrangement comprising 13 protein-coding genes, 21 tRNAs, and 2 rRNAs. No internal stop codon was found in the protein-coding genes. Phylogenetic tree analysis revealed that Malayan gaur is more closely related to Burmese banteng instead of gaur.
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 Genome sequence and comparative pathogenomics analysis of a Salmonella enterica Serovar Typhi strain associated with a typhoid carrier in Malaysia

Yap KP, Gan HM, Teh CS, Baddam R, Chai LC, Kumar N, et al.

J Bacteriol, 2012 Nov;194(21):5970-1.
PMID: 23045488 DOI: 10.1128/JB.01416-12

Salmonella enterica serovar Typhi is a human pathogen that causes typhoid fever predominantly in developing countries. In this article, we describe the whole genome sequence of the S. Typhi strain CR0044 isolated from a typhoid fever carrier in Kelantan, Malaysia. These data will further enhance the understanding of its host persistence and adaptive mechanism.
Changes in rumen protozoal community by condensed tannin fractions of different molecular weights from a Leucaena leucocephala hybrid in vitro

Saminathan M, Gan HM, Abdullah N, Wong CMVL, Ramiah SK, Tan HY, et al.

J Appl Microbiol, 2017 Apr 23.
PMID: 28434189 DOI: 10.1111/jam.13477

AIMS: To evaluate the effects of condensed tannins (CTs) fractions of differing molecular weights (MWs) from a Leucaena leucocephala hybrid-Rendang on the rumen protozoal community in vitro.
METHODS AND RESULTS: The effects of unfractionated CTs (F0) and CT fractions of different MWs (F1 > F2 > F3 > F4 > F5) on protozoal population and community were evaluated in vitro using rumen microbes and ground guinea grass as the substrate. Higher-MW CT fractions F1 and F2 significantly (P
Fulltext Genomic characterization of eight Ensifer strains isolated from pristine caves and a whole genome phylogeny of Ensifer (Sinorhizobium)

Kumar HK, Gan HM, Tan MH, Eng WW, Barton HA, Hudson AO, et al.

J Genomics, 2017;5:12-15.
PMID: 28138345 DOI: 10.7150/jgen.17863

A total of eight Ensifer sp. strains were isolated from two pristine cave environments. One strain was isolated from a cave water pool located in the Wind Cave National Park, South Dakota, USA and the remaining seven strains were isolated from Lechuguilla Cave of Carlsbad Caverns National Park, New Mexico, USA. Whole genome sequencing and comparative genomic analyses of the eight isolates compared to various type strains from the genera Ensifer and Sinorhizobium demonstrates that although members in these genera can be phylogenetically separated into two distinct clades, the percentage of conserved proteins (POCP) between various type strains from Ensifer and Sinorhizobium are consistently higher than 50%, providing strong genomic evidence to support the classification of the genera Ensifer and Sinorhizobium into a single genus.
ORDER within the chaos: Insights into phylogenetic relationships within the Anomura (Crustacea: Decapoda) from mitochondrial sequences and gene order rearrangements

Tan MH, Gan HM, Lee YP, Linton S, Grandjean F, Bartholomei-Santos ML, et al.

Mol Phylogenet Evol, 2018 10;127:320-331.
PMID: 29800651 DOI: 10.1016/j.ympev.2018.05.015

The infraorder Anomura consists of a morphologically and ecologically heterogeneous group of decapod crustaceans, and has attracted interest from taxonomists for decades attempting to find some order out of the seemingly chaotic diversity within the group. Species-level diversity within the Anomura runs the gamut from the "hairy" spindly-legged yeti crab found in deep-sea hydrothermal vent environments to the largest known terrestrial invertebrate, the robust coconut or robber crab. Owing to a well-developed capacity for parallel evolution, as evidenced by the occurrence of multiple independent carcinization events, Anomura has long tested the patience and skill of both taxonomists attempting to find order, and phylogeneticists trying to establish stable hypotheses of evolutionary inter-relationships. In this study, we performed genome skimming to recover the mitogenome sequences of 12 anomuran species including the world's largest extant invertebrate, the robber crab (Birgus latro), thereby over doubling these resources for this group, together with 8 new brachyuran mitogenomes. Maximum-likelihood (ML) and Bayesian-inferred (BI) phylogenetic reconstructions based on amino acid sequences from mitogenome protein-coding genes provided strong support for the monophyly of the Anomura and Brachyura and their sister relationship, consistent with previous studies. The majority of relationships within families were supported and were largely consistent with current taxonomic classifications, whereas many relationships at higher taxonomic levels were unresolved. Nevertheless, we have strong support for a polyphyletic Paguroidea and recovered a well-supported clade of a subset of paguroids (Diogenidae + Coenobitidae) basal to all other anomurans, though this requires further testing with greater taxonomic sampling. We also introduce a new feature to the MitoPhAST bioinformatics pipeline (https://github.com/mht85/MitoPhAST) that enables the extraction of mitochondrial gene order (MGO) information directly from GenBank files and clusters groups based on common MGOs. Using this tool, we compared MGOs across the Anomura and Brachyura, identifying Anomura as a taxonomic "hot spot" with high variability in MGOs among congeneric species from multiple families while noting the broad association of highly-rearranged MGOs with several anomuran lineages inhabiting extreme niches. We also demonstrate the value of MGOs as a source of novel synapomorphies for independently reinforcing tree-based relationships and for shedding light on relationships among challenging groups such as the Aegloidea and Lomisoidea that were unresolved in phylogenetic reconstructions. Overall, this study contributes a substantial amount of new genetic material for Anomura and attempts to further resolve anomuran evolutionary relationships where possible based on a combination of sequence and MGO information. The new feature in MitoPhAST adds to the relatively limited number of bioinformatics tools available for MGO analyses, which can be utilized widely across animal groups.
A new set of microsatellite markers for Phoxinus lumaireul senso lato, Phoxinus marsilii and Phoxinus krkae for population and molecular taxonomic studies

Vucić M, Jelić M, Klobučar G, Jelić D, Gan HM, Austin C, et al.

J Fish Biol, 2022 Nov;101(5):1225-1234.
PMID: 36054289 DOI: 10.1111/jfb.15194

Minnows of the genus Phoxinus are common and an often highly abundant fish species in Palearctic freshwater habitats. Phoxinus species have a complex evolutionary history, phylogenetic relationships are not well understood and there are a number of unresolved taxonomic problems. There are currently 23 different mitochondrial genetic lineages identified in the genus Phoxinus, 13 of which are recognized as valid species. The taxonomic status of these lineages requires resolution, including the degree to which they can interbreed. Suitable nuclear molecular markers for studies of population divergence and interbreeding between morphotypes and mitochondrial lineages are lacking for Phoxinus species. Therefore, the authors developed a set of microsatellite markers using genomic information from Phoxinus lumaireul and tested their suitability for this and two related species, Phoxinus krkae and Phoxinus marsilii. Out of 16 microsatellite candidate loci isolated, 12 were found to be in Hardy-Weinberg equilibrium when tested on two P. lumaireul senso lato populations. Seven loci amplified across the three species, enabling the study of intraspecific genetic diversity and population structure within P. marsilii and P. krkae. The markers were able to clearly resolve differences among the three tested species, including the recently described P. krkae, and are therefore suitable for the detection of introgression and hybridization among populations consisting of mixtures of two or more of P. lumaireul s. l., P. marsilii and P. krkae.
Fulltext Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a Giant Phage Mutant Collection

Gan HM, Eng WWH, Barton MK, Adams LE, Samsudin NA, Bartl AJ, et al.

Genome Announc, 2017 Aug 24;5(34).
PMID: 28839032 DOI: 10.1128/genomeA.00857-17

We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097, which we utilize for genetic analyses of giant bacterial viruses. Our analyses identified several genetic variations between the two strains, most significantly confirming strain TT6675 as a serine suppressor and TT9097 as a nonsuppressor.
Fulltext Impact of dengue virus (DENV) co-infection on clinical manifestations, disease severity and laboratory parameters

Dhanoa A, Hassan SS, Ngim CF, Lau CF, Chan TS, Adnan NA, et al.

BMC Infect Dis, 2016 08 11;16(1):406.
PMID: 27514512 DOI: 10.1186/s12879-016-1731-8

BACKGROUND: The co-circulation of 4 DENV serotypes in geographically expanding area, has resulted in increasing occurrence of DENV co-infections. However, studies assessing the clinical impact of DENV co-infections have been scarce and have involved small number of patients. This study explores the impact of DENV co-infection on clinical manifestations and laboratory parameters.
METHODS: This retrospective study involved consecutive hospitalized patients with non-structural protein 1 (NS1) antigen positivity during an outbreak (Jan to April 2014). Multiplex RT-PCR was performed directly on NS1 positive serum samples to detect and determine the DENV serotypes. All PCR-positive serum samples were inoculated onto C6/36 cells. Multiplex PCR was repeated on the supernatant of the first blind passage of the serum-infected cells. Random samples of supernatant from the first passage of C6/36 infected cells were subjected to whole genome sequencing. Clinical and laboratory variables were compared between patients with and without DENV co-infections.
RESULTS: Of the 290 NS1 positive serum samples, 280 were PCR positive for DENV. Medical notes of 262 patients were available for analysis. All 4 DENV serotypes were identified. Of the 262 patients, forty patients (15.3 %) had DENV co-infections: DENV-1/DENV-2(85 %), DENV-1/DENV-3 (12.5 %) and DENV-2/DENV-3 (2.5 %). Another 222 patients (84.7 %) were infected with single DENV serotype (mono-infection), with DENV- 1 (76.6 %) and DENV- 2 (19.8 %) predominating. Secondary dengue infections occurred in 31.3 % patients. Whole genome sequences of random samples representing DENV-1 and DENV-2 showed heterogeneity amongst the DENVs. Multivariate analysis revealed that pleural effusion and the presence of warning signs were significantly higher in the co-infected group, both in the overall and subgroup analysis. Diarrhoea was negatively associated with co-infection. Additionally, DENV-2 co-infected patients had higher frequency of patients with severe thrombocytopenia (platelet count < 50,000/mm(3)), whereas DENV-2 mono-infections presented more commonly with myalgia. Elevated creatinine levels were more frequent amongst the co-infected patients in univariate analysis. Haemoconcentration and haemorrhagic manifestations were not higher amongst the co-infected patients. Serotypes associated with severe dengue were: DENV-1 (n = 9), DENV-2 (n = 1), DENV-3 (n = 1) in mono-infected patients and DENV-1/DENV-2 (n = 5) and DENV-1/DENV-3 (n = 1) amongst the co-infected patients.
CONCLUSION: DENV co-infections are not uncommon in a hyperendemic region and co-infected patients are skewed towards more severe clinical manifestations compared to mono-infected patients.
Fulltext Genome Sequence ofSerratia marcescenssubsp.sakuensisStrain K27, a Marine Bacterium Isolated from Sponge (Haliclona amboinensis)

Cheng TH, Saidin J, Danish-Daniel M, Gan HM, Mat Isa MN, Abu Bakar MF, et al.

Genome Announc, 2018 Feb 08;6(6).
PMID: 29439033 DOI: 10.1128/genomeA.00022-18

Serratia marcescens
subsp.sakuensisstrain K27 was isolated from sponge (Haliclona amboinensis). The genome of this strain consists of 5,325,727 bp, with 5,140 open reading frames (ORFs), 3 rRNAs, and 67 tRNAs. It contains genes for the production of amylases, lipases, and proteases. Gene clusters for the biosynthesis of nonribosomal peptides and thiopeptide were also identified.
Temporal changes in arthropod activity in tropical anthropogenic forests

Brandon-Mong GJ, Littlefair JE, Sing KW, Lee YP, Gan HM, Clare EL, et al.

Bull. Entomol. Res., 2018 Dec;108(6):792-799.
PMID: 29441836 DOI: 10.1017/S000748531800010X

Arthropod communities in the tropics are increasingly impacted by rapid changes in land use. Because species showing distinct seasonal patterns of activity are thought to be at higher risk of climate-related extirpation, global warming is generally considered a lower threat to arthropod biodiversity in the tropics than in temperate regions. To examine changes associated with land use and weather variables in tropical arthropod communities, we deployed Malaise traps at three major anthropogenic forests (secondary reserve forest, oil palm forest, and urban ornamental forest (UOF)) in Peninsular Malaysia and collected arthropods continuously for 12 months. We used metabarcoding protocols to characterize the diversity within weekly samples. We found that changes in the composition of arthropod communities were significantly associated with maximum temperature in all the three forests, but shifts were reversed in the UOF compared with the other forests. This suggests arthropods in forests in Peninsular Malaysia face a double threat: community shifts and biodiversity loss due to exploitation and disturbance of forests which consequently put species at further risk related to global warming. We highlight the positive feedback mechanism of land use and temperature, which pose threats to the arthropod communities and further implicates ecosystem functioning and human well-being. Consequently, conservation and mitigation plans are urgently needed.
Fulltext Complete chloroplast genome data of Shorea macrophylla (Engkabang): Structural features, comparative and phylogenetic analysis

Chew IYY, Chung HH, Lim LWK, Lau MML, Gan HM, Wee BS, et al.

Data Brief, 2023 Apr;47:109029.
PMID: 36936629 DOI: 10.1016/j.dib.2023.109029

Shorea macrophylla belongs to the Shorea genus under the Dipterocarpaceae family. It is a woody tree that grows in the rainforest in Southeast Asia. The complete chloroplast (cp) genome sequence of S. macrophylla is reported here. The genomic size of S. macrophylla is 150,778 bp and it possesses a circular structure with conserved constitute regions of large single copy (LSC, 83,681 bp) and small single copy (SSC, 19,813 bp) regions, as well as a pair of inverted repeats with a length of 23,642 bp. It has 112 unique genes, including 78 protein-coding genes, 30 tRNA genes, and four rRNA genes. The genome exhibits a similar GC content, gene order, structure, and codon usage when compared to previously reported chloroplast genomes from other plant species. The chloroplast genome of S. macrophylla contained 262 SSRs, the most prevalent of which was A/T, followed by AAT/ATT. Furthermore, the sequences contain 43 long repeat sequences, practically most of them are forward or palindrome type long repeats. The genome structure of S. macrophylla was compared to the genomic structures of closely related species from the same family, and eight mutational hotspots were discovered. The phylogenetic analysis demonstrated a close relationship between Shorea and Parashorea species, indicating that Shorea is not monophyletic. The complete chloroplast genome sequence analysis of S. macrophylla reported in this paper will contribute to further studies in molecular identification, genetic diversity, and phylogenetic research.
Fulltext A multiplexed RT-PCR assay for nanopore whole genome sequencing of Tilapia lake virus (TiLV)

Delamare-Deboutteville J, Meemetta W, Pimsannil K, Sangpo P, Gan HM, Mohan CV, et al.

Sci Rep, 2023 Nov 20;13(1):20276.
PMID: 37985860 DOI: 10.1038/s41598-023-47425-w

Tilapia lake virus (TiLV) is a highly contagious viral pathogen that affects tilapia, a globally significant and affordable source of fish protein. To prevent the introduction and spread of TiLV and its impact, there is an urgent need for increased surveillance, improved biosecurity measures, and continuous development of effective diagnostic and rapid sequencing methods. In this study, we have developed a multiplexed RT-PCR assay that can amplify all ten complete genomic segments of TiLV from various sources of isolation. The amplicons generated using this approach were immediately subjected to real-time sequencing on the Nanopore system. By using this approach, we have recovered and assembled 10 TiLV genomes from total RNA extracted from naturally TiLV-infected tilapia fish, concentrated tilapia rearing water, and cell culture. Our phylogenetic analysis, consisting of more than 36 TiLV genomes from both newly sequenced and publicly available TiLV genomes, provides new insights into the high genetic diversity of TiLV. This work is an essential steppingstone towards integrating rapid and real-time Nanopore-based amplicon sequencing into routine genomic surveillance of TiLV, as well as future vaccine development.
Fulltext Insight Into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere

Gan HM, Szegedi E, Fersi R, Chebil S, Kovács L, Kawaguchi A, et al.

Front Microbiol, 2019;10:1896.
PMID: 31456792 DOI: 10.3389/fmicb.2019.01896

Crown gall (CG) is a globally distributed and economically important disease of grapevine and other important crop plants. The causal agent of CG is Agrobacterium or Allorhizobium strains that harbor a tumor-inducing plasmid (pTi). The microbial community within the CG tumor has not been widely elucidated and it is not known if certain members of this microbial community promote or inhibit CG. This study investigated the microbiotas of grapevine CG tumor tissues from seven infected vineyards located in Hungary, Japan, Tunisia, and the United States. Heavy co-amplification of grapevine chloroplast and mitochondrial ribosomal RNA genes was observed with the widely used Illumina V3-V4 16S rRNA gene primers, requiring the design of a new reverse primer to enrich for bacterial 16S rRNA from CG tumors. The operational taxonomic unit (OTU) clustering approach is not suitable for CG microbiota analysis as it collapsed several ecologically distinct Agrobacterium species into a single OTU due to low interspecies genetic divergence. The CG microbial community assemblages were significantly different across sampling sites (ANOSIM global R = 0.63, p-value = 0.001) with evidence of site-specific differentially abundant ASVs. The presence of Allorhizobium vitis in the CG microbiota is almost always accompanied by Xanthomonas and Novosphingobium, the latter may promote the spread of pTi plasmid by way of acyl-homoserine lactone signal production, whereas the former may take advantage of the presence of substrates associated with plant cell wall growth and repair. The technical and biological insights gained from this study will contribute to the understanding of complex interaction between the grapevine and its microbial community and may facilitate better management of CG disease in the future.

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