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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 Pleistocene divergence across a mountain range and the influence of selection on mitogenome evolution in threatened Australian freshwater cod species

Harrisson K, Pavlova A, Gan HM, Lee YP, Austin CM, Sunnucks P

Heredity (Edinb), 2016 Jun;116(6):506-15.
PMID: 26883183 DOI: 10.1038/hdy.2016.8

Climatic differences across a taxon's range may be associated with specific bioenergetic demands and may result in genetics-based metabolic adaptation, particularly in aquatic ectothermic organisms that rely on heat exchange with the environment to regulate key physiological processes. Extending down the east coast of Australia, the Great Dividing Range (GDR) has a strong influence on climate and the evolutionary history of freshwater fish species. Despite the GDR acting as a strong contemporary barrier to fish movement, many species, and species with shared ancestries, are found on both sides of the GDR, indicative of historical dispersal events. We sequenced complete mitogenomes from the four extant species of the freshwater cod genus Maccullochella, two of which occur on the semi-arid, inland side of the GDR, and two on the mesic coastal side. We constructed a dated phylogeny and explored the relative influences of purifying and positive selection in the evolution of mitogenome divergence among species. Results supported mid- to late-Pleistocene divergence of Maccullochella across the GDR (220-710 thousand years ago), bringing forward previously reported dates. Against a background of pervasive purifying selection, we detected potentially functionally relevant fixed amino acid differences across the GDR. Although many amino acid differences between inland and coastal species may have become fixed under relaxed purifying selection in coastal environments rather than positive selection, there was evidence of episodic positive selection acting on specific codons in the Mary River coastal lineage, which has consistently experienced the warmest and least extreme climate in the genus.
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 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.
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 Purifying selection and genetic drift shaped Pleistocene evolution of the mitochondrial genome in an endangered Australian freshwater fish

Pavlova A, Gan HM, Lee YP, Austin CM, Gilligan DM, Lintermans M, et al.

Heredity (Edinb), 2017 05;118(5):466-476.
PMID: 28051058 DOI: 10.1038/hdy.2016.120

Genetic variation in mitochondrial genes could underlie metabolic adaptations because mitochondrially encoded proteins are directly involved in a pathway supplying energy to metabolism. Macquarie perch from river basins exposed to different climates differ in size and growth rate, suggesting potential presence of adaptive metabolic differences. We used complete mitochondrial genome sequences to build a phylogeny, estimate lineage divergence times and identify signatures of purifying and positive selection acting on mitochondrial genes for 25 Macquarie perch from three basins: Murray-Darling Basin (MDB), Hawkesbury-Nepean Basin (HNB) and Shoalhaven Basin (SB). Phylogenetic analysis resolved basin-level clades, supporting incipient speciation previously inferred from differentiation in allozymes, microsatellites and mitochondrial control region. The estimated time of lineage divergence suggested an early- to mid-Pleistocene split between SB and the common ancestor of HNB+MDB, followed by mid-to-late Pleistocene splitting between HNB and MDB. These divergence estimates are more recent than previous ones. Our analyses suggested that evolutionary drivers differed between inland MDB and coastal HNB. In the cooler and more climatically variable MDB, mitogenomes evolved under strong purifying selection, whereas in the warmer and more climatically stable HNB, purifying selection was relaxed. Evidence for relaxed selection in the HNB includes elevated transfer RNA and 16S ribosomal RNA polymorphism, presence of potentially mildly deleterious mutations and a codon (ATP6113) displaying signatures of positive selection (ratio of nonsynonymous to synonymous substitution rates (dN/dS) >1, radical change of an amino-acid property and phylogenetic conservation across the Percichthyidae). In addition, the difference could be because of stronger genetic drift in the smaller and historically more subdivided HNB with low per-population effective population sizes.
Fulltext Prevalence and Disability-Adjusted Life Year Rates of Asthma in China: Findings from the GBD Study 2019 of the G20

Liu M, Gan H, Lin Y, Lin R, Xue M, Zhang T, et al.

Int J Environ Res Public Health, 2022 Nov 08;19(22).
PMID: 36429381 DOI: 10.3390/ijerph192214663

BACKGROUND: The credible materials about the burden of asthma in China when compared to other countries in the group of twenty (G20) remain unavailable.
OBJECTIVES AND DESIGN: Following the popular analysis strategy used in the Global Burden of Disease Study, the age-, sex-, country-specific prevalence, and disability-adjusted life years (DALYs) of asthma in China were analyzed. Meanwhile, the comparison in trends between China and other countries in the G20 was also evaluated.
RESULTS: In 2019, asthma was the 8th leading cause of the DALYs' burden of 369 diseases in China. From 1990 to 2019, the age-standardized prevalence and DALY rates of asthma in China decreased by 14% and 51%, respectively; further, the decline rate of DALYs was much higher than the global average (-51%: -43%). It is worth noting that the overall population age-standardized DALYs rate of asthma in China was the lowest in the G20 during 2019 (102.81, 95% UI: (72.30,147.42)/100,000). Moreover, the age-standardized asthma prevalence rate peaks in both childhood (178.14, 95% UI: (90.50, 329.01)/100,000) and the elderly (541.80, 95% UI: (397.79, 679.92)/100,000). Moreover, throughout the study, subjects in the 5 to 9 years old interval were a constant focus of our attention.
CONCLUSIONS: The disease burden of asthma has varied greatly by gender and age over the past 30 years. In contrast to the increasing burden in most other G20 countries, the age-standardized prevalence rate of asthma shows a significant decreasing trend in China, however, the age-standardized DALYs rate shows a fluctuating change, and has even shown a rebound trend in recent years.
Bacterial community structure, predicted metabolic activities, and formation of volatile compounds attributed to Malaysian fish sauce flavour

Shanti Dwita Lestari, Shobirin Meor Hussin A, Mustafa S, Yun Shin Sew, Ming Gan H, Hashim AM, et al.

Food Chem, 2023 Nov 15;426:136568.
PMID: 37437500 DOI: 10.1016/j.foodchem.2023.136568

The fermentation of Malaysian fish sauce (budu) varies from one to twelve months depending on the producer, resulting in inconsistent quality. The microbiota, their predicted metabolic pathways and volatile metabolites profiles were determined at different stages of budu fermentation. Budu fermented for 1 and 3 months were characterized by the presence of Gram negative Enterobacterales, Gammaproteobacteria, and Fusobacteriaceae, which continuously decrease in abundance over fermentation time. The metabolic pathways prediction grouped 1- and 3- month budu in a cluster enriched with degradation reactions. 6-month budu were dominated by Halanaerobium and Staphylococcus, while the 12-month were dominated by Lentibacillus, Bacilli, and Halomonas. Biosynthesis-type predicted pathways involving protein and lipid derivatives were enriched in 6- and 12-month fermented budu, accumulating 2,6-dimethylpyrazine, methyl 2-ethyldecanoate, 2-phenylacetaldehyde, 3-methylbutanal, and 3-methylbutanoic acid. These compounds may indicate budu maturity and quality. This result may assist as a reference for quality control and fermentation monitoring.
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
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.