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Fulltext Discovery of Known and Novel Viruses in Wild and Cultivated Blueberry in Florida through Viral Metagenomic Approaches

Saad N, Olmstead JW, Varsani A, Polston JE, Jones JB, Folimonova SY, et al.

Viruses, 2021 Jun 18;13(6).
PMID: 34207047 DOI: 10.3390/v13061165

Southern highbush blueberry (interspecific hybrids of Vaccinium corymbosum L.) is cultivated near wild V. corymbosum as well as closely related species in Florida, USA. The expansion of blueberry cultivation into new areas in Florida and deployment of new cultivars containing viruses can potentially increase the diversity of viruses in wild and cultivated V. corymbosum. In this study, viral diversity in wild and cultivated blueberries (V. corymbosum) is described using a metagenomic approach. RNA viromes from V. corymbosum plants collected from six locations (two cultivated and four wild) in North Central Florida were generated by high throughput sequencing (HTS) and analyzed using a bioinformatic analysis pipeline. De novo assembled contigs obtained from viromes of both commercial and wild sites produced sequences with similarities to plant virus species from a diverse range of families (Amalgaviridae, Caulimoviridae, Endornaviridae, Ophioviridae, Phenuiviridae, and Virgaviridae). In addition, this study has enabled the identification of blueberry latent virus (BlLV) and blueberry mosaic associated ophiovirus (BlMaV) for the first time in Florida, as well as a tentative novel tepovirus (blueberry virus T) (BlVT) in blueberry. To the best of our knowledge, this is the first study that compares viral diversity in wild and cultivated blueberry using a metagenomic approach.

Matched MeSH terms: Metagenome*; Metagenomics/methods*
Fulltext High-Throughput Sequencing-Based Investigation of Viruses in Human Cancers by Multienrichment Approach

Mollerup S, Asplund M, Friis-Nielsen J, Kjartansdóttir KR, Fridholm H, Hansen TA, et al.

J Infect Dis, 2019 09 13;220(8):1312-1324.
PMID: 31253993 DOI: 10.1093/infdis/jiz318

BACKGROUND: Viruses and other infectious agents cause more than 15% of human cancer cases. High-throughput sequencing-based studies of virus-cancer associations have mainly focused on cancer transcriptome data.
METHODS: In this study, we applied a diverse selection of presequencing enrichment methods targeting all major viral groups, to characterize the viruses present in 197 samples from 18 sample types of cancerous origin. Using high-throughput sequencing, we generated 710 datasets constituting 57 billion sequencing reads.
RESULTS: Detailed in silico investigation of the viral content, including exclusion of viral artefacts, from de novo assembled contigs and individual sequencing reads yielded a map of the viruses detected. Our data reveal a virome dominated by papillomaviruses, anelloviruses, herpesviruses, and parvoviruses. More than half of the included samples contained 1 or more viruses; however, no link between specific viruses and cancer types were found.
CONCLUSIONS: Our study sheds light on viral presence in cancers and provides highly relevant virome data for future reference.

Matched MeSH terms: Metagenome/genetics*
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
Fulltext Effect of ethnicity and socioeconomic variation to the gut microbiota composition among pre-adolescent in Malaysia

Chong CW, Ahmad AF, Lim YA, Teh CS, Yap IK, Lee SC, et al.

Sci Rep, 2015;5:13338.
PMID: 26290472 DOI: 10.1038/srep13338

Gut microbiota plays an important role in mammalian host metabolism and physiological functions. The functions are particularly important in young children where rapid mental and physical developments are taking place. Nevertheless, little is known about the gut microbiome and the factors that contribute to microbial variation in the gut of South East Asian children. Here, we compared the gut bacterial richness and composition of pre-adolescence in Northern Malaysia. Our subjects covered three distinct ethnic groups with relatively narrow range of socioeconomic discrepancy. These included the Malays (n = 24), Chinese (n = 17) and the Orang Asli (indigenous) (n = 20). Our results suggested a strong ethnicity and socioeconomic-linked bacterial diversity. Highest bacterial diversity was detected from the economically deprived indigenous children while the lowest diversity was recorded from the relatively wealthy Chinese children. In addition, predicted functional metagenome profiling suggested an over-representation of pathways pertinent to bacterial colonisation and chemotaxis in the former while the latter exhibited enriched gene pathways related to sugar metabolism.

Matched MeSH terms: Metagenome
Fulltext Microbiome and Biocatalytic Bacteria in Monkey Cup (Nepenthes Pitcher) Digestive Fluid

Chan XY, Hong KW, Yin WF, Chan KG

Sci Rep, 2016 Jan 28;6:20016.
PMID: 26817720 DOI: 10.1038/srep20016

Tropical carnivorous plant, Nepenthes, locally known as "monkey cup", utilises its pitcher as a passive trap to capture insects. It then secretes enzymes into the pitcher fluid to digest the insects for nutrients acquisition. However, little is known about the microbiota and their activity in its pitcher fluid. Eighteen bacteria phyla were detected from the metagenome study in the Nepenthes pitcher fluid. Proteobacteria, Bacteroidetes and Actinobacteria are the dominant phyla in the Nepenthes pitcher fluid. We also performed culturomics approach by isolating 18 bacteria from the Nepenthes pitcher fluid. Most of the bacterial isolates possess chitinolytic, proteolytic, amylolytic, and cellulolytic and xylanolytic activities. Fifteen putative chitinase genes were identified from the whole genome analysis on the genomes of the 18 bacteria isolated from Nepenthes pitcher fluid and expressed for chitinase assay. Of these, six clones possessed chitinase activity. In conclusion, our metagenome result shows that the Nepenthes pitcher fluid contains vast bacterial diversity and the culturomic studies confirmed the presence of biocatalytic bacteria within the Nepenthes pitcher juice which may act in symbiosis for the turn over of insects trapped in the Nepenthes pitcher fluid.

Matched MeSH terms: Metagenome
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*
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
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*
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
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
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
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
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*
Fulltext Global monitoring of antimicrobial resistance based on metagenomics analyses of urban sewage

Hendriksen RS, Munk P, Njage P, van Bunnik B, McNally L, Lukjancenko O, et al.

Nat Commun, 2019 03 08;10(1):1124.
PMID: 30850636 DOI: 10.1038/s41467-019-08853-3

Antimicrobial resistance (AMR) is a serious threat to global public health, but obtaining representative data on AMR for healthy human populations is difficult. Here, we use metagenomic analysis of untreated sewage to characterize the bacterial resistome from 79 sites in 60 countries. We find systematic differences in abundance and diversity of AMR genes between Europe/North-America/Oceania and Africa/Asia/South-America. Antimicrobial use data and bacterial taxonomy only explains a minor part of the AMR variation that we observe. We find no evidence for cross-selection between antimicrobial classes, or for effect of air travel between sites. However, AMR gene abundance strongly correlates with socio-economic, health and environmental factors, which we use to predict AMR gene abundances in all countries in the world. Our findings suggest that global AMR gene diversity and abundance vary by region, and that improving sanitation and health could potentially limit the global burden of AMR. We propose metagenomic analysis of sewage as an ethically acceptable and economically feasible approach for continuous global surveillance and prediction of AMR.

Matched MeSH terms: Metagenome*; Metagenomics/methods
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
The impact of tropical forest logging and oil palm agriculture on the soil microbiome

Tripathi BM, Edwards DP, Mendes LW, Kim M, Dong K, Kim H, et al.

Mol Ecol, 2016 May;25(10):2244-57.
PMID: 26994316 DOI: 10.1111/mec.13620

Selective logging and forest conversion to oil palm agriculture are rapidly altering tropical forests. However, functional responses of the soil microbiome to these land-use changes are poorly understood. Using 16S rRNA gene and shotgun metagenomic sequencing, we compared composition and functional attributes of soil biota between unlogged, once-logged and twice-logged rainforest, and areas converted to oil palm plantations in Sabah, Borneo. Although there was no significant effect of logging history, we found a significant difference between the taxonomic and functional composition of both primary and logged forests and oil palm. Oil palm had greater abundances of genes associated with DNA, RNA, protein metabolism and other core metabolic functions, but conversely, lower abundance of genes associated with secondary metabolism and cell-cell interactions, indicating less importance of antagonism or mutualism in the more oligotrophic oil palm environment. Overall, these results show a striking difference in taxonomic composition and functional gene diversity of soil microorganisms between oil palm and forest, but no significant difference between primary forest and forest areas with differing logging history. This reinforces the view that logged forest retains most features and functions of the original soil community. However, networks based on strong correlations between taxonomy and functions showed that network complexity is unexpectedly increased due to both logging and oil palm agriculture, which suggests a pervasive effect of both land-use changes on the interaction of soil microbes.

Matched MeSH terms: Metagenome
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
Acclimatisation-induced stress influenced host metabolic and gut microbial composition change

Yap IK, Kho MT, Lim SH, Ismail NH, Yam WK, Chong CW

Mol Biosyst, 2015 Jan;11(1):297-306.
PMID: 25382376 DOI: 10.1039/c4mb00463a

Understanding the basal gut bacterial community structure and the host metabolic composition is pivotal for the interpretation of laboratory treatments designed to answer questions pertinent to host-microbe interactions. In this study, we report for the first time the underlying gut microbiota and systemic metabolic composition in BALB/c mice during the acclimatisation period. Our results showed that stress levels were reduced in the first three days of the study when the animals were subjected to repetitive handling daily but the stress levels were increased when handling was carried out at lower frequencies (weekly). We also observed a strong influence of stress on the host metabolism and commensal compositional variability. In addition, temporal biological compartmental variations in the responses were observed. Based on these results, we suggest that consistency in the frequency and duration of laboratory handling is crucial in murine models to minimise the impact of stress levels on the commensal and host metabolism dynamics. Furthermore, caution is advised in consideration of the temporal delay effect when integrating metagenomics and metabonomics data across different biological matrices (i.e. faeces and urine).

Matched MeSH terms: Metagenome
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*
From the High Arctic to the Equator: Do Soil Metagenomes Differ According to Our Expectations?

Kerfahi D, Tripathi BM, Dong K, Kim M, Kim H, Ferry Slik JW, et al.

Microb Ecol, 2019 Jan;77(1):168-185.
PMID: 29882154 DOI: 10.1007/s00248-018-1215-z

Comparing the functional gene composition of soils at opposite extremes of environmental gradients may allow testing of hypotheses about community and ecosystem function. Here, we were interested in comparing how tropical microbial ecosystems differ from those of polar climates. We sampled several sites in the equatorial rainforest of Malaysia and Brunei, and the high Arctic of Svalbard, Canada, and Greenland, comparing the composition and the functional attributes of soil biota between the two extremes of latitude, using shotgun metagenomic Illumina HiSeq2000 sequencing. Based upon "classical" views of how tropical and higher latitude ecosystems differ, we made a series of predictions as to how various gene function categories would differ in relative abundance between tropical and polar environments. Results showed that in some respects our predictions were correct: the polar samples had higher relative abundance of dormancy related genes, and lower relative abundance of genes associated with respiration, and with metabolism of aromatic compounds. The network complexity of the Arctic was also lower than the tropics. However, in various other respects, the pattern was not as predicted; there were no differences in relative abundance of stress response genes or in genes associated with secondary metabolism. Conversely, CRISPR genes, phage-related genes, and virulence disease and defense genes, were unexpectedly more abundant in the Arctic, suggesting more intense biotic interaction. Also, eukaryote diversity and bacterial diversity were higher in the Arctic of Svalbard compared to tropical Brunei, which is consistent with what may expected from amplicon studies in terms of the higher pH of the Svalbard soil. Our results in some respects confirm expectations of how tropical versus polar nature may differ, and in other respects challenge them.

Matched MeSH terms: Metagenome/genetics*; Metagenome/physiology*

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