Displaying publications 1 - 20 of 39 in total

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  1. A metagenome for lacustrine Cladophora (Cladophorales) reveals remarkable diversity of eukaryotic epibionts and genes relevant to materials cycling
    Graham LE, Knack JJ, Graham ME, Graham JM, Zulkifly S
    J Phycol, 2015 Jun;51(3):408-18.
    PMID: 26986658 DOI: 10.1111/jpy.12296
    Periphyton dominated by the cellulose-rich filamentous green alga Cladophora forms conspicuous growths along rocky marine and freshwater shorelines worldwide, providing habitat for diverse epibionts. Bacterial epibionts have been inferred to display diverse functions of biogeochemical significance: N-fixation and other redox reactions, phosphorus accumulation, and organic degradation. Here, we report taxonomic diversity of eukaryotic and prokaryotic epibionts and diversity of genes associated with materials cycling in a Cladophora metagenome sampled from Lake Mendota, Dane Co., WI, USA, during the growing season of 2012. A total of 1,060 distinct 16S, 173 18S, and 351 28S rRNA operational taxonomic units, from which >220 genera or species of bacteria (~60), protists (~80), fungi (6), and microscopic metazoa (~80), were distinguished with the use of reference databases. We inferred the presence of several algal taxa generally associated with marine systems and detected Jaoa, a freshwater periphytic ulvophyte previously thought endemic to China. We identified six distinct nifH gene sequences marking nitrogen fixation, >25 bacterial and eukaryotic cellulases relevant to sedimentary C-cycling and technological applications, and genes encoding enzymes in aerobic and anaerobic pathways for vitamin B12 biosynthesis. These results emphasize the importance of Cladophora in providing habitat for microscopic metazoa, fungi, protists, and bacteria that are often inconspicuous, yet play important roles in ecosystem biogeochemistry.
    Matched MeSH terms: Metagenome
  2. Metagenomic Analysis of the Effect of Enteromorpha prolifera Bloom on Microbial Community and Function in Aquaculture Environment
    Sun F, Wang C, Chen H, Zheng Z
    Curr Microbiol, 2020 May;77(5):816-825.
    PMID: 31927597 DOI: 10.1007/s00284-019-01862-x
    Enteromorpha prolifera blooms considerably affected coastal environments in recent years. However, the effects of E. prolifera on microbial ecology and function remained unknown. In this study, metagenomic sequencing was used to investigate the effect of E. prolifera bloom on the microbial communities and functional genes in an aquaculture environment. Results showed that E. prolifera bloom could significantly alter the microbial composition and abundance, and heterotrophic bacteria comprised the major groups in the E. prolifera bloom pond, which was dominated by Actinomycetales and Flavobacteriales. The study indicated that viruses played an important role in shaping the microbial community and diversity during E. prolifera bloom. These viruses affected various dominant microbial taxa (such as Rhodobacteraceae, Synechococcus, and Prochlorococcus), which produced an obvious impact on potential nutrient transformation. Functional annotation analysis indicated that E. prolifera bloom would considerably shift the metabolism function by altering the structure and abundance of the microbial community. E. prolifera bloom pond had the low ability of potential metabolic capabilities of nitrogen, sulfur, and phosphate, whereas promoted gene abundance of genetic information processing. These changes in the microbial community and function could produce serious effect on aquaculture ecosystem.
    Matched MeSH terms: Metagenome*; Metagenomics
  3. Probiotic consumption relieved human stress and anxiety symptoms possibly via modulating the neuroactive potential of the gut microbiota
    Ma T, Jin H, Kwok LY, Sun Z, Liong MT, Zhang H
    Neurobiol Stress, 2021 May;14:100294.
    PMID: 33511258 DOI: 10.1016/j.ynstr.2021.100294
    Stress has been shown to disturb the balance of human intestinal microbiota and subsequently causes mental health problems like anxiety and depression. Our previous study showed that ingesting the probiotic strain, Lactobacillus (L.) plantarum P-8, for 12 weeks could alleviate stress and anxiety of stressed adults. The current study was a follow-up work aiming to investigate the functional role of the gut metagenomes in the observed beneficial effects. The fecal metagenomes of the probiotic (n = 43) and placebo (n = 36) receivers were analyzed in depth. The gut microbiomes of the placebo group at weeks 0 and 12 showed a significantly greater Aitchison distance (P 
    Matched MeSH terms: Metagenome
  4. Fulltext Insights into microbial community structure and diversity in oil palm waste compost
    Khalid NA, Rajandas H, Parimannan S, Croft LJ, Loke S, Chong CS, et al.
    3 Biotech, 2019 Oct;9(10):364.
    PMID: 31588388 DOI: 10.1007/s13205-019-1892-4
    Empty fruit bunch (EFB) and palm oil mill effluent (POME) are the major wastes generated by the oil palm industry in Malaysia. The practice of EFB and POME digester sludge co-composting has shown positive results, both in mitigating otherwise environmentally damaging waste streams and producing a useful product (compost) from these streams. In this study, the bacterial ecosystems of 12-week-old EFB-POME co-compost and POME biogas sludge from Felda Maokil, Johor were analysed using 16S metagenome sequencing. Over ten phyla were detected, with Chloroflexi being the predominant phylum, representing approximately 53% of compost and 23% of the POME microbiome reads. The main bacterial lineage found in the compost and POME was Anaerolinaceae (Chloroflexi) with 30% and 18% of the total gene fragments, respectively. The significant differences between compost and POME communities were abundances of Syntrophobacter, Sulfuricurvum and Coprococcus. No methanogens were identified due to the bias in general 16S primers to eubacteria. The preponderance of anaerobic species in the compost and high abundance of secondary metabolite fermenting bacteria is due to an extended composting time, with anaerobic collapse of the pile due to the tropical heat. Predictive functional profiles of the metagenomes using 16S rRNA marker genes suggest that the presence of enzymes involved in degradation of polysaccharides such as glucoamylase, endoglucanase and arabinofuranosidase, all of which were strongly active in POME. Eubacterial species associated with cellulytic methanogenesis were present in both samples.
    Matched MeSH terms: Metagenome
  5. Fulltext Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition
    Ahmad MF, Abdullah H, Hassan MN, Jamaludin MI, Sivam A, Komatsu K, et al.
    Int J Mol Sci, 2023 Jan 03;24(1).
    PMID: 36614337 DOI: 10.3390/ijms24010872
    Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.
    Matched MeSH terms: Metagenome
  6. Editorial: metagenome-assembled genomes in non-alcoholic fatty liver disease
    Chan WK, Wong VW
    Aliment Pharmacol Ther, 2021 03;53(6):755-756.
    PMID: 33599321 DOI: 10.1111/apt.16280
    Matched MeSH terms: Metagenome
  7. Fulltext An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
    Axtner J, Crampton-Platt A, Hörig LA, Mohamed A, Xu CCY, Yu DW, et al.
    Gigascience, 2019 Apr 01;8(4).
    PMID: 30997489 DOI: 10.1093/gigascience/giz029
    BACKGROUND: The use of environmental DNA for species detection via metabarcoding is growing rapidly. We present a co-designed lab workflow and bioinformatic pipeline to mitigate the 2 most important risks of environmental DNA use: sample contamination and taxonomic misassignment. These risks arise from the need for polymerase chain reaction (PCR) amplification to detect the trace amounts of DNA combined with the necessity of using short target regions due to DNA degradation.

    FINDINGS: Our high-throughput workflow minimizes these risks via a 4-step strategy: (i) technical replication with 2 PCR replicates and 2 extraction replicates; (ii) using multi-markers (12S,16S,CytB); (iii) a "twin-tagging," 2-step PCR protocol; and (iv) use of the probabilistic taxonomic assignment method PROTAX, which can account for incomplete reference databases. Because annotation errors in the reference sequences can result in taxonomic misassignment, we supply a protocol for curating sequence datasets. For some taxonomic groups and some markers, curation resulted in >50% of sequences being deleted from public reference databases, owing to (i) limited overlap between our target amplicon and reference sequences, (ii) mislabelling of reference sequences, and (iii) redundancy. Finally, we provide a bioinformatic pipeline to process amplicons and conduct PROTAX assignment and tested it on an invertebrate-derived DNA dataset from 1,532 leeches from Sabah, Malaysia. Twin-tagging allowed us to detect and exclude sequences with non-matching tags. The smallest DNA fragment (16S) amplified most frequently for all samples but was less powerful for discriminating at species rank. Using a stringent and lax acceptance criterion we found 162 (stringent) and 190 (lax) vertebrate detections of 95 (stringent) and 109 (lax) leech samples.

    CONCLUSIONS: Our metabarcoding workflow should help research groups increase the robustness of their results and therefore facilitate wider use of environmental and invertebrate-derived DNA, which is turning into a valuable source of ecological and conservation information on tetrapods.

    Matched MeSH terms: Metagenome*; Metagenomics/methods*
  8. Fulltext Genome-Centric Metagenomic Insights into the Impact of Alkaline/Acid and Thermal Sludge Pretreatment on the Microbiome in Digestion Sludge
    Liang Z, Shi J, Wang C, Li J, Liang D, Yong EL, et al.
    Appl Environ Microbiol, 2020 11 10;86(23).
    PMID: 32948522 DOI: 10.1128/AEM.01920-20
    Pretreatment of waste-activated sludge (WAS) is an effective way to destabilize sludge floc structure and release organic matter for improving sludge digestion efficiency. Nonetheless, information on the impact of WAS pretreatment on digestion sludge microbiomes, as well as mechanistic insights into how sludge pretreatment improves digestion performance, remains elusive. In this study, a genome-centric metagenomic approach was employed to investigate the digestion sludge microbiome in four sludge digesters with different types of feeding sludge: WAS pretreated with 0.25 mol/liter alkaline/acid (APAD), WAS pretreated with 0.8 mol/liter alkaline/acid (HS-APAD), thermally pretreated WAS (thermal-AD), and fresh WAS (control-AD). We retrieved 254 metagenome-assembled genomes (MAGs) to identify the key functional populations involved in the methanogenic digestion process. These MAGs span 28 phyla, including 69 yet-to-be-cultivated lineages, and 30 novel lineages were characterized with metabolic potential associated with hydrolysis and fermentation. Interestingly, functional populations involving carbohydrate digestion were enriched in APAD and HS-APAD, while lineages related to protein and lipid fermentation were enriched in thermal-AD, corroborating the idea that different substrates are released from alkaline/acid and thermal pretreatments. Among the major functional populations (i.e., fermenters, syntrophic acetogens, and methanogens), significant correlations between genome sizes and abundance of the fermenters were observed, particularly in APAD and HS-APAD, which had improved digestion performance.IMPORTANCE Wastewater treatment generates large amounts of waste-activated sludge (WAS), which consists mainly of recalcitrant microbial cells and particulate organic matter. Though WAS pretreatment is an effective way to release sludge organic matter for subsequent digestion, detailed information on the impact of the sludge pretreatment on the digestion sludge microbiome remains scarce. Our study provides unprecedented genome-centric metagenomic insights into how WAS pretreatments change the digestion sludge microbiomes, as well as their metabolic networks. Moreover, digestion sludge microbiomes could be a unique source for exploring microbial dark matter. These results may inform future optimization of methanogenic sludge digestion and resource recovery.
    Matched MeSH terms: Metagenome*
  9. Fulltext Oligosaccharides might contribute to the antidiabetic effect of honey: a review of the literature
    Erejuwa OO, Sulaiman SA, Wahab MS
    Molecules, 2011 Dec 28;17(1):248-66.
    PMID: 22205091 DOI: 10.3390/molecules17010248
    Evidence shows that honey improves glycemic control in diabetes mellitus. Besides its hypoglycemic effect, studies indicate that honey ameliorates lipid abnormalities in rats and humans with diabetes. The majority of these studies do not examine the mechanisms by which honey ameliorates glycemic and/or lipid derangements. The gut microbiota is now recognized for its ability to increase energy harvest from the diet and alter lipid metabolism of the host. Recently available data implicate a causal role of these gut microbes in the pathophysiology of obesity, insulin resistance, and diabetes mellitus. In this review, we present some of the latest findings linking gut microbiota to pathogenesis of obesity, insulin resistance, and diabetes mellitus. The review also underlines data that demonstrate the beneficial effects of oligosaccharides on various abnormalities commonly associated with these disorders. Based on the similarities of some of these findings with those of honey, together with the evidence that honey contains oligosaccharides, we hypothesize that oligosaccharides present in honey might contribute to the antidiabetic and other health-related beneficial effects of honey. We anticipate that the possibility of oligosaccharides in honey contributing to the antidiabetic and other health-related effects of honey will stimulate a renewed research interest in this field.
    Matched MeSH terms: Metagenome/drug effects; Metagenome/physiology
  10. Fulltext Soup to Tree: The Phylogeny of Beetles Inferred by Mitochondrial Metagenomics of a Bornean Rainforest Sample
    Crampton-Platt A, Timmermans MJ, Gimmel ML, Kutty SN, Cockerill TD, Vun Khen C, et al.
    Mol Biol Evol, 2015 Sep;32(9):2302-16.
    PMID: 25957318 DOI: 10.1093/molbev/msv111
    In spite of the growth of molecular ecology, systematics and next-generation sequencing, the discovery and analysis of diversity is not currently integrated with building the tree-of-life. Tropical arthropod ecologists are well placed to accelerate this process if all specimens obtained through mass-trapping, many of which will be new species, could be incorporated routinely into phylogeny reconstruction. Here we test a shotgun sequencing approach, whereby mitochondrial genomes are assembled from complex ecological mixtures through mitochondrial metagenomics, and demonstrate how the approach overcomes many of the taxonomic impediments to the study of biodiversity. DNA from approximately 500 beetle specimens, originating from a single rainforest canopy fogging sample from Borneo, was pooled and shotgun sequenced, followed by de novo assembly of complete and partial mitogenomes for 175 species. The phylogenetic tree obtained from this local sample was highly similar to that from existing mitogenomes selected for global coverage of major lineages of Coleoptera. When all sequences were combined only minor topological changes were induced against this reference set, indicating an increasingly stable estimate of coleopteran phylogeny, while the ecological sample expanded the tip-level representation of several lineages. Robust trees generated from ecological samples now enable an evolutionary framework for ecology. Meanwhile, the inclusion of uncharacterized samples in the tree-of-life rapidly expands taxon and biogeographic representation of lineages without morphological identification. Mitogenomes from shotgun sequencing of unsorted environmental samples and their associated metadata, placed robustly into the phylogenetic tree, constitute novel DNA "superbarcodes" for testing hypotheses regarding global patterns of diversity.
    Matched MeSH terms: Metagenome
  11. Fulltext Resistance and resilience of small-scale recirculating aquaculture systems (RAS) with or without algae to pH perturbation
    Mohamed Ramli N, Giatsis C, Md Yusoff F, Verreth J, Verdegem M
    PLoS One, 2018;13(4):e0195862.
    PMID: 29659617 DOI: 10.1371/journal.pone.0195862
    The experimental set-up of this study mimicked recirculating aquaculture systems (RAS) where water quality parameters such as dissolved oxygen, pH, temperature, and turbidity were controlled and wastes produced by fish and feeding were converted to inorganic forms. A key process in the RAS was the conversion of ammonia to nitrite and nitrite to nitrate through nitrification. It was hypothesized that algae inclusion in RAS would improve the ammonia removal from the water; thereby improving RAS water quality and stability. To test this hypothesis, the stability of the microbiota community composition in a freshwater RAS with (RAS+A) or without algae (RAS-A) was challenged by introducing an acute pH drop (from pH 7 to 4 during three hours) to the system. Stigeoclonium nanum, a periphytic freshwater microalga was used in this study. No significant effect of the algae presence was found on the resistance to the acute pH drop on ammonia conversion to nitrite and nitrite conversion to nitrate. Also the resilience of the ammonia conversion to the pH drop disruption was not affected by the addition of algae. This could be due to the low biomass of algae achieved in the RAS. However, with regard to the conversion step of nitrite to nitrate, RAS+A was significantly more resilient than RAS-A. In terms of overall bacterial communities, the composition and predictive function of the bacterial communities was significantly different between RAS+A and RAS-A.
    Matched MeSH terms: Metagenome
  12. Fulltext Comparative assessment of faecal microbial composition and metabonome of swine, farmers and human control
    Tan SC, Chong CW, Yap IKS, Thong KL, Teh CSJ
    Sci Rep, 2020 Jun 02;10(1):8997.
    PMID: 32488118 DOI: 10.1038/s41598-020-65891-4
    The gastrointestinal tract of humans and swine consist of a wide range of bacteria which interact with hosts metabolism. Due to the differences in co-evolution and co-adaptation, a large fraction of the gut microbiome is host-specific. In this study, we evaluated the effect of close human-animal interaction to the faecal metagenome and metabonome of swine, farmer and human control. Three distinct clusters were observed based on T-RFLP-derived faecal microbial composition. However, 16S-inferred faecal microbiota and metabolic profiles showed that only human control was significantly different from the swine (P 
    Matched MeSH terms: Metagenome/genetics
  13. High-throughput terrestrial biodiversity assessments: mitochondrial metabarcoding, metagenomics or metatranscriptomics?
    Wilson JJ, Brandon-Mong GJ, Gan HM, Sing KW
    Mitochondrial DNA A DNA Mapp Seq Anal, 2019 01;30(1):60-67.
    PMID: 29591722 DOI: 10.1080/24701394.2018.1455189
    Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.
    Matched MeSH terms: Metagenome*
  14. Fulltext Preventing sexually transmitted infections: back to basics
    Rompalo A
    J Clin Invest, 2011 Dec;121(12):4580-3.
    PMID: 22133882 DOI: 10.1172/JCI61592
    Sexually transmitted infections (STIs) have plagued humans for millennia and can result in chronic disease, pregnancy complications, infertility, and even death. Recent technological advances have led to a better understanding of the causative agents for these infections as well as aspects of their pathogenesis that might represent novel therapeutic targets. The articles in this Review Series provide excellent updates on the recent advances in understanding of the pathogenesis of some very important and persistent STIs and discuss the importance of considering each pathogen in the broader context of the environment of the individual who it infects.
    Matched MeSH terms: Metagenome
  15. Microbiota composition data for wild and captive bluestreak cleaner wrasse Labroides dimidiatus (Valenciennes, 1839)
    Okomoda VT, Nurul ANA, Danish-Daniel AM, Oladimeji AS, Abol-Munafi AB, Alabi KI, et al.
    Data Brief, 2020 Oct;32:106120.
    PMID: 32817873 DOI: 10.1016/j.dib.2020.106120
    The Labroides dimidiatus is known as the "doctor fish" because of its role in removing parasites and infectious pathogens from the body of other fishes. This important role played both in wild and captive conditions could represent a novel form of parasitic transmission process mediated by the cleaning activity of the fish. Yet, there is a paucity of data on the microflora associated with this fish which is important for tracking disease infection and generally monitoring the health status of the fish. This article, therefore, represents the first dataset for the microbiota composition of wild and captive L. dimidiatus. Wild fish samples and carriage water were gotten in Terengganu Malaysia around the corals of the Karah Island. The captive sample, however, was obtained from well-known ornamental fish suppliers in Terengganu Malaysia. Thereafter, bacteria present on the skin, in the stomach and the aquarium water were enumerated using culture-independent approaches and Next Generation Sequencing (NGS) technology. Data obtained from the three metagenomic libraries using NGS analysis gave 1,426,740 amplicon sequence reads which are composed of 508 operational taxonomic units (OTUs) for wild samples and 3,238,564 valid reads and 828 OTUs for captive samples. All sequence reads were deposited in the GeneBank (Accession numbers SAMN14260247, SAMN14260248, SAMN14260249, SAMN14260250, SAMN14260251, and SAMN14260252). The dataset presented is associated with the research article "16S rDNA-Based Metagenomic Analysis of Microbial Communities Associated with Wild Labroides dimidiatus From Karah Island, Terengganu, Malaysia" [1]. The microbiota data presented in this article can be used to monitor the health and wellbeing of the ornamental fish, especially under captivity, hence preventing possible cross-infection.
    Matched MeSH terms: Metagenome
  16. Fulltext Helminth colonization is associated with increased diversity of the gut microbiota
    Lee SC, Tang MS, Lim YA, Choy SH, Kurtz ZD, Cox LM, et al.
    PLoS Negl Trop Dis, 2014 May;8(5):e2880.
    PMID: 24851867 DOI: 10.1371/journal.pntd.0002880
    Soil-transmitted helminths colonize more than 1.5 billion people worldwide, yet little is known about how they interact with bacterial communities in the gut microbiota. Differences in the gut microbiota between individuals living in developed and developing countries may be partly due to the presence of helminths, since they predominantly infect individuals from developing countries, such as the indigenous communities in Malaysia we examine in this work. We compared the composition and diversity of bacterial communities from the fecal microbiota of 51 people from two villages in Malaysia, of which 36 (70.6%) were infected by helminths. The 16S rRNA V4 region was sequenced at an average of nineteen thousand sequences per samples. Helminth-colonized individuals had greater species richness and number of observed OTUs with enrichment of Paraprevotellaceae, especially with Trichuris infection. We developed a new approach of combining centered log-ratio (clr) transformation for OTU relative abundances with sparse Partial Least Squares Discriminant Analysis (sPLS-DA) to enable more robust predictions of OTU interrelationships. These results suggest that helminths may have an impact on the diversity, bacterial community structure and function of the gut microbiota.
    Matched MeSH terms: Metagenome/genetics
  17. Metagenomics analysis reveals significant modulation of cecal microbiota of broilers fed palm kernel expeller diets
    Chen WL, Tang SGH, Jahromi MF, Candyrine SCL, Idrus Z, Abdullah N, et al.
    Poult Sci, 2019 Jan 01;98(1):56-68.
    PMID: 30137571 DOI: 10.3382/ps/pey366
    The potential use of palm kernel expeller (PKE) as an alternative energy source in broiler diets is limited by the high fiber content. Although enzymatic treatment could alleviate the fiber component and increase the nutritive value of PKE, this apparent improvement is not reflected in the growth response of birds fed with the treated-PKE. As chicken's ceca are the most heavily populated with microflora within their gastrointestinal tract, it was hypothesized that any modulation of the intestinal environment by dietary treatments should be reflected by the composition and activities of the cecal microflora. There is a correlation between cecal microbiota composition and the efficiency of the host to extract energy from the diet and to deposit that energy into improved feed conversion ratio. At present, little is known about the changes on cecal microflora of broilers fed with PKE diets. Hence, this study was designed to assess the effects of feeding different forms of PKE; namely untreated PKE (UPKE), enzyme-treated PKE (EPKE), and oligosaccharides extracted from PKE (OligoPKE), on the cecal microbiota of broiler chickens at 14 d old (day 14) and 28 d old (day 28) using 16S rRNA gene high-throughput next-generation sequencing method. The results showed that temporal changes in cecal microbiota of broiler chickens were evident on day 14 and day 28. The relative abundance of phylum Firmicutes, known to be involved in nutrient uptake and absorption in both age groups was higher in the UPKE as compared to EPKE group. In addition, supplementation of OligoPKE increased (P < 0.05) the relative abundance of Lactobacillus on both D14 and D28, signifying its effect as prebiotics in enhancing growth of indigenous Lactobacillus. Our results showed that cecal microbiota was significantly modulated by dietary treatments and that the lower relative abundance of phylum Firmicutes in chickens fed with EPKE could be a reason why broiler chickens fed with EPKE of higher metabolizable energy (ME) content did not show improvement in their growth performance.
    Matched MeSH terms: Metagenome*
  18. Fulltext Insights into the ecological roles and evolution of methyl-coenzyme M reductase-containing hot spring Archaea
    Hua ZS, Wang YL, Evans PN, Qu YN, Goh KM, Rao YZ, et al.
    Nat Commun, 2019 10 08;10(1):4574.
    PMID: 31594929 DOI: 10.1038/s41467-019-12574-y
    Several recent studies have shown the presence of genes for the key enzyme associated with archaeal methane/alkane metabolism, methyl-coenzyme M reductase (Mcr), in metagenome-assembled genomes (MAGs) divergent to existing archaeal lineages. Here, we study the mcr-containing archaeal MAGs from several hot springs, which reveal further expansion in the diversity of archaeal organisms performing methane/alkane metabolism. Significantly, an MAG basal to organisms from the phylum Thaumarchaeota that contains mcr genes, but not those for ammonia oxidation or aerobic metabolism, is identified. Together, our phylogenetic analyses and ancestral state reconstructions suggest a mostly vertical evolution of mcrABG genes among methanogens and methanotrophs, along with frequent horizontal gene transfer of mcr genes between alkanotrophs. Analysis of all mcr-containing archaeal MAGs/genomes suggests a hydrothermal origin for these microorganisms based on optimal growth temperature predictions. These results also suggest methane/alkane oxidation or methanogenesis at high temperature likely existed in a common archaeal ancestor.
    Matched MeSH terms: Metagenome*
  19. Fulltext Genomic and metagenomic signatures of giant viruses are ubiquitous in water samples from sewage, inland lake, waste water treatment plant, and municipal water supply in Mumbai, India
    Chatterjee A, Sicheritz-Pontén T, Yadav R, Kondabagil K
    Sci Rep, 2019 03 06;9(1):3690.
    PMID: 30842490 DOI: 10.1038/s41598-019-40171-y
    We report the detection of genomic signatures of giant viruses (GVs) in the metagenomes of three environment samples from Mumbai, India, namely, a pre-filter of a household water purifier, a sludge sample from wastewater treatment plant (WWTP), and a drying bed sample of the same WWTP. The de novo assembled contigs of each sample yielded 700 to 2000 maximum unique matches with the GV genomic database. In all three samples, the maximum number of reads aligned to Pandoraviridae, followed by Phycodnaviridae, Mimiviridae, Iridoviridae, and other Megaviruses. We also isolated GVs from every environmental sample (n = 20) we tested using co-culture of the sample with Acanthomoeba castellanii. From this, four randomly selected GVs were subjected to the genomic characterization that showed remarkable cladistic homology with the three GV families viz., Mimivirirdae (Mimivirus Bombay [MVB]), Megaviruses (Powai lake megavirus [PLMV] and Bandra megavius [BAV]), and Marseilleviridae (Kurlavirus [KV]). All 4 isolates exhibited remarkable genomic identity with respective GV families. Functionally, the genomes were indistinguishable from other previously reported GVs, encoding nearly all COGs across extant family members. Further, the uncanny genomic homogeneity exhibited by individual GV families across distant geographies indicate their yet to be ascertained ecological significance.
    Matched MeSH terms: Metagenome*
  20. Fulltext A metagenomic comparison of clearwater, probiotic, and Rapid BFTTM on Pacific whiteleg shrimp, Litopenaeus vannamei cultures
    Waiho K, Abd Razak MS, Abdul Rahman MZ, Zaid Z, Ikhwanuddin M, Fazhan H, et al.
    PeerJ, 2023;11:e15758.
    PMID: 37790619 DOI: 10.7717/peerj.15758
    Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFTTM with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFTTM and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFTTM) in shrimp culture.
    Matched MeSH terms: Metagenome
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