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1. Quinone redox cycling drives lignocellulose depolymerization and degradation in composting environments based on metagenomics analysis

Author:
Ru Sun; Ziyi Cao; Xiaoli Wen; Liangcai Ma; Yucheng Zhou; Jixuan Li; Mengxin Fu; Pengfei Zhu; Kecheng Li; Qunliang Li
Source:
Science of the total environment 2023 v.856 pp. 159009
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Actinobacteria; cellulose; depolymerization; environment; hemicellulose; lignin; lignocellulose; quinones;     Show all 9 Subjects
Abstract:
... In this study, the effect of Fe³⁺ on the quinone redox cycling driving lignocellulosic degradation in composting systems was investigated. The results showed that the degradation rates of cellulose, hemicellulose, and lignin were higher in the experimental group (CT) with Fe₂(SO₄)₃ addition than in the blank group (CK) (CT, 52.55 %, 45.14 %, 56.98 %; CK, 49.63 %, 37.34 %, 52.3 %). Changes in the a ...
DOI:
10.1016/j.scitotenv.2022.159009

2. A proposed framework for the identification of indicator genes for monitoring antibiotic resistance in wastewater: Insights from metagenomic sequencing

Author:
Mehedi Hasan Tarek; Emily Garner
Source:
Science of the total environment 2023 v.854 pp. 158698
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; animal and human health; antibiotic resistance; environment; monitoring; municipal wastewater;     Show all 6 Subjects
Abstract:
... Antibiotic resistance is one of the greatest threats to global human and animal health of our time. Municipal wastewater has been identified as a hotspot of antibiotic resistance contamination to water bodies. However, there are numerous potential antibiotic resistant pathogens and their associated antibiotic resistance genes (ARGs), making it difficult to implement routine monitoring that address ...
DOI:
10.1016/j.scitotenv.2022.158698

3. Dissecting giant hailstones: A glimpse into the troposphere with its diverse bacterial communities and fibrous microplastics

Author:
Marko Kozjek; Damjan Vengust; Tina Radošević; Gregor Žitko; Simon Koren; Nataša Toplak; Ivan Jerman; Matej Butala; Matejka Podlogar; Manca Kovač Viršek
Source:
Science of the total environment 2023 v.856 pp. 158786
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Raman spectroscopy; bacterial communities; electron microscopy; environment; hail; ice; microplastics; sand; troposphere; Slovenia;     Show all 11 Subjects
Abstract:
... The formation of giant hailstones is a rare weather event that has devastating consequences in inhabited areas. This hazard has been occurring more frequently and with greater size of hailstones in recent years, and thus needs to be better understood. While the generally accepted mechanism is thought to be a process similar to the formation of smaller hailstones but with exceptional duration and s ...
DOI:
10.1016/j.scitotenv.2022.158786

4. The community assembly for understanding the viral-assisted response of bacterial community to Cr-contamination in soils

Author:
Shuyue Liu; Yu Shi; Mingming Sun; Dan Huang; Wensheng Shu; Mao Ye
Source:
Journal of hazardous materials 2023 v.441 pp. 129975
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; chromium; evolution; microbial communities; slags; soil; soil pollution; species diversity; variance; virus assembly; viruses; China;     Show all 12 Subjects
Abstract:
... Microbial community assembly contributes to the restoration and rehabilitation of the disturbed ecosystems. However, the viral assembly mechanism and its difference from bacterial communities under soil contamination have not been previously reported. Here, clean, light and heavy chromium (Cr)-contaminated soils were collected from two Cr slag sites and adjacent soils in northwestern and southwest ...
DOI:
10.1016/j.jhazmat.2022.129975

5. Ecological life strategies of microbes in response to antibiotics as a driving factor in soils

Author:
Udita Sharma; Deepak Rawat; Paromita Mukherjee; Furqan Farooqi; Vandana Mishra; Radhey Shyam Sharma
Source:
Science of the total environment 2023 v.854 pp. 158791
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Actinobacteria; Bacteroidetes; Firmicutes; Proteobacteria; antibiotic resistance; ecosystems; environmental factors; metabolism; microbial communities; models; phenotype; selection pressure; soil;     Show all 14 Subjects
Abstract:
... Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communi ...
DOI:
10.1016/j.scitotenv.2022.158791

6. Iron scraps packing rapidly enhances nitrogen removal in an aerobic sludge system and the mechanism

Author:
Xin Yu; Hong Chen; Yunfan Liu; Luying Yu; Kai Wang; Gang Xue
Source:
Science of the total environment 2023 v.856 pp. 159081
ISSN:
0048-9697
Subject:
metagenomics,   etc   ; Nitrosomonas; Thauera; carbon; denitrification; energy; environment; gene expression; iron; microbial communities; nitrate reduction; nitrification; nitrogen; sludge; total nitrogen; transcriptomics;     Show all 16 Subjects
Abstract:
... Simultaneous nitrification and denitrification (SND) has the advantage of energy saving and carbon demand reduction. Here, readily available low-cost iron scraps packing was added to an aerobic sludge system. This successfully enhanced the efficiency of total nitrogen removal from 37.7 ± 13.2 % to 62.7 ± 7.9 % over 2 days. While electrons from iron biocorrosion did not contribute to nitrate reduct ...
DOI:
10.1016/j.scitotenv.2022.159081

7. Biogeography and diversity patterns of antibiotic resistome in the sediments of global lakes

Author:
Chang Liu; Jinping Chen; Yuyi Yang; Yanguo Teng; Haiyang Chen
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 421-430
ISSN:
1001-0742
Subject:
metagenomics,   etc   ; Enterobacteriaceae; antibiotic resistance; antibiotic resistance genes; antibiotics; bacterial communities; biogeography; community structure; data collection; lakes; risk; sediments; stochastic processes; China;     Show all 14 Subjects
Abstract:
... Lakes act as one of the reservoirs and dispersal routes of antibiotic resistance genes (ARGs) and pathogenic resistant bacteria in aquatic environments. Previous studies reported the occurrence and distribution of ARGs in lakes worldwide; however, few investigated the biogeography and diversity patterns of antibiotic resistome in the environment. To fill this gap, a large-scale data set of sedimen ...
DOI:
10.1016/j.jes.2022.06.024

8. Novel electro-assisted micro-aerobic cathode biological technology induces oxidative demethylation of N, N-dimethylformamide for efficient ammonification of refractory membrane-making wastewater

Author:
Guang Yang; Hui Xu; Yudong Luo; Shengqiang Hei; Guangqing Song; Xia Huang
Source:
Journal of hazardous materials 2023 v.442 pp. 130001
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; acidification; aeration; ammonia; ammonification; ammonium nitrogen; biochemical pathways; biodegradation; cathodes; chemical oxygen demand; demethylation; fermentation; hydrolysis; microbial communities; nitrification; oxygen; toxicology; wastewater;     Show all 18 Subjects
Abstract:
... Recalcitrant and toxicological membrane-making wastewater displays negative impacts on environment, and this is difficult to treat efficiently using conventional hydrolytic acidification. In this study, a novel electro-assisted biological reactor with micro-aerobic cathode (EABR-MAC) was developed to improve the biodegradation and ammonification of N, N-dimethylformamide (DMF) in membrane-making w ...
DOI:
10.1016/j.jhazmat.2022.130001

9. The plastisphere microbiome in alpine soils alters the microbial genetic potential for plastic degradation and biogeochemical cycling

Author:
Joel Rüthi; Basil M. Rast; Weihong Qi; Carla Perez-Mon; Lucrezia Pardi-Comensoli; Ivano Brunner; Beat Frey
Source:
Journal of hazardous materials 2023 v.441 pp. 129941
ISSN:
0304-3894
Subject:
metagenomics,   etc   ; ammonium; biodegradability; biodegradation; carboxylesterase; genes; genetic traits; lignin; lipids; metabolism; microbiome; nitrates; nitrification; nitrites; nitrogen fixation; peptidoglycans; polyethylene; secretion; soil; soil microorganisms;     Show all 20 Subjects
Abstract:
... Plastic is exceedingly abundant in soils, but little is known about its ecological consequences for soil microbiome functioning. Here we report the impacts of polyethylene and biodegradable Ecovio and BI-OPL plastic films buried in alpine soils for 5 months on the genetic potential of the soil microbiome using shotgun metagenomics. The microbiome was more affected by Ecovio and BI-OPL than by poly ...
DOI:
10.1016/j.jhazmat.2022.129941

10. Genome-resolved metagenomic analysis reveals different functional potentials of multiple Candidatus Brocadia species in a full-scale swine wastewater treatment system

Author:
Yabing Meng; Depeng Wang; Zhong Yu; Qingyun Yan; Zhili He; Fangang Meng
Source:
Frontiers of environmental science & engineering 2023 v.17 no.1 pp. 2
ISSN:
2095-2201
Subject:
metagenomics,   etc   ; acetate kinase; acetates; ammonia; ammonium; anaerobic ammonium oxidation; carbon; cyanase; dominant species; ecological differentiation; hydroxylamine; nitrite reductase; nitrites; organic nitrogen; phylogeny; sequence analysis; swine; urease; wastewater treatment;     Show all 19 Subjects
Abstract:
... The increasing application of anammox processes suggests their enormous potential for nitrogen removal in wastewater treatment facilities. However, the functional potentials and ecological differentiation of cooccurring anammox species in complex ecosystems have not been well elucidated. Herein, by utilizing functional reconstruction and comparative genome analysis, we deciphered the cooccurring m ...
DOI:
10.1007/s11783-023-1602-7

11. Polysaccharide extract from Rosa laevigata fruit attenuates inflammatory obesity by targeting redox balance and gut interface in high-fat diet-fed rats

Author:
Xuejiao Zhang; Chenzhong Jin; Han Liu; Yihong Hu; Yunyun Zhou; Weiguo Wu; Si Qin
Source:
Food science and human wellness 2023 v.12 no.2 pp. 442-453
ISSN:
2213-4530
Subject:
metagenomics,   etc   ; Lachnospiraceae; Prevotella; Rosa laevigata; body weight changes; chemoprevention; digestive system; food science; fruits; functional foods; humans; intestinal microorganisms; liver function; multiomics; obesity; phenotype; polysaccharides; sequence analysis; Asia;     Show all 19 Subjects
Abstract:
... Low-molecular-weight polysaccharides (RLPs) extracted from Rosa laevigata fruits showed multiple biofunctions in Asia. This study aimed to investigate its anti-inflammatory obesity effect in high-fat diet-fed rats and further elucidated the underlying molecular mechanism by multi-omics methods. The results showed that RLPs administration had significantly restored immune organ indexes and reduced ...
DOI:
10.1016/j.fshw.2022.07.046

12. Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city

Author:
Yanchu Ke; Wenjun Sun; Zibo Jing; Zhinan Zhao; Shuguang Xie
Source:
Journal of environmental sciences (China) 2023 v.127 pp. 714-725
ISSN:
1001-0742
Subject:
metagenomics,   etc   ; Achromobacter; Mycobacterium; Stenotrophomonas; ammonia; antibiotic resistance; antibiotic resistance genes; antibiotics; autumn; biofilm; community structure; hardness; microbial communities; plasmids; plate count; seasonal variation; spring; suburban areas; summer; temperature; total organic carbon; water distribution; water treatment; winter; China;     Show all 25 Subjects
Abstract:
... Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial commun ...
DOI:
10.1016/j.jes.2022.07.001

13. Effects of BDE-209 exposure on growth performance, intestinal digestive enzymes, and intestinal microbiome in common carp (Cyprinus carpio L.)

Author:
Xulu Chang; Meiru Kang; Junchang Feng; Jianxin Zhang; Xianfeng Wang
Source:
Aquaculture and fisheries 2023 v.8 no.1 pp. 33-41
ISSN:
2468-550X
Subject:
metagenomics,   etc   ; Bacteroides; Clostridium; Cyprinus carpio; Fusobacteria; Lactobacillus; Rhodopseudomonas; Shewanella; amylases; aquaculture; bacteria; carboxylic ester hydrolases; decabromodiphenyl ether; endocrine system; fish; fish health; growth performance; intestinal microorganisms; intestines; oxidative stress; pollutants; probiotics; proteinases; short chain fatty acids; species diversity; wildlife;     Show all 26 Subjects
Abstract:
... Polybrominated diphenyl ether has become a widespread environmental pollutant in aquatic environments. BDE-209, a prominent PBDEs found in the environment and wildlife, has been proven to cause oxidative stress, immune damage and endocrine system disorders in fish. However, the effects of BDE-209 on the intestinal health of fish remain unclear. This research aimed to determine the effects of BDE-2 ...
DOI:
10.1016/j.aaf.2021.05.005

14. Beyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security

Author:
Mark A. Chapman; Yuqi He; Meiliang Zhou
Source:
The new phytologist 2022 v.234 no.5 pp. 1583-1597
ISSN:
0028-646X
Subject:
metagenomics,   etc   ; climate change; nutrition;     Show all 3 Subjects
Abstract:
... Underutilized crops are, by definition, under‐researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress‐tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Ta ...
DOI:
10.1111/nph.18021

15. HiCBin: binning metagenomic contigs and recovering metagenome-assembled genomes using Hi-C contact maps

Author:
Yuxuan Du; Fengzhu Sun
Source:
Genome biology 2022 v.23 no.1 pp. 63
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; algorithms; chromosomes; genome;     Show all 4 Subjects
Abstract:
... Recovering high-quality metagenome-assembled genomes (MAGs) from complex microbial ecosystems remains challenging. Recently, high-throughput chromosome conformation capture (Hi-C) has been applied to simultaneously study multiple genomes in natural microbial communities. We develop HiCBin, a novel open-source pipeline, to resolve high-quality MAGs utilizing Hi-C contact maps. HiCBin employs the Hi ...
DOI:
10.1186/s13059-022-02626-w

16. High-throughput approaches to understand and engineer bacteriophages

Author:
Phil Huss; Jackie Chen; Srivatsan Raman
Source:
Trends in biochemical sciences 2022 pp. -
ISSN:
0968-0004
Subject:
metagenomics,   etc   ; bacteriophages; face; genome;     Show all 4 Subjects
Abstract:
... Bacteriophage research has been vital to fundamental aspects of modern biology. Advances in metagenomics have revealed treasure troves of new and uncharacterized bacteriophages ('phages') that are not yet understood. However, our ability to find new phages has outpaced our understanding of how sequence encodes function in phages. Traditional approaches for characterizing phages are limited in scal ...
DOI:
10.1016/j.tibs.2022.08.012

17. Music of metagenomics—a review of its applications, analysis pipeline, and associated tools [Erratum: February 2022, v.22(1); p.137]

Author:
Bilal Wajid; Faria Anwar; Imran Wajid; Haseeb Nisar; Sharoze Meraj; Ali Zafar; Mustafa Kamal Al-Shawaqfeh; Ali Riza Ekti; Asia Khatoon; Jan S. Suchodolski
Source:
Functional & integrative genomics 2022 v.22 no.1 pp. 3-26
ISSN:
1438-793X
Subject:
metagenomics,   etc   ; ecosystems; genome; music; taxonomy;     Show all 5 Subjects
Abstract:
... This humble effort highlights the intricate details of metagenomics in a simple, poetic, and rhythmic way. The paper enforces the significance of the research area, provides details about major analytical methods, examines the taxonomy and assembly of genomes, emphasizes some tools, and concludes by celebrating the richness of the ecosystem populated by the “metagenome.” ...
DOI:
10.1007/s10142-021-00810-y

18. Nanopore adaptive sampling: a tool for enrichment of low abundance species in metagenomic samples

Author:
Samuel Martin; Darren Heavens; Yuxuan Lan; Samuel Horsfield; Matthew D. Clark; Richard M. Leggett
Source:
Genome biology 2022 v.23 no.1 pp. 11
ISSN:
1474-760X
Subject:
metagenomics,   etc   ; genome; mathematical models; nanopores;     Show all 4 Subjects
Abstract:
... Adaptive sampling is a method of software-controlled enrichment unique to nanopore sequencing platforms. To test its potential for enrichment of rarer species within metagenomic samples, we create a synthetic mock community and construct sequencing libraries with a range of mean read lengths. Enrichment is up to 13.87-fold for the least abundant species in the longest read length library; factorin ...
DOI:
10.1186/s13059-021-02582-x

19. Numerous variants of leucine rich repeats in proteins from nucleo-cytoplasmic large DNA viruses

Author:
Norio Matsushima; Robert H. Kretsinger
Source:
Gene 2022 v.817 pp. 146156
ISSN:
0378-1119
Subject:
metagenomics,   etc   ; DNA; cysteine; genes; hydrophobicity; leucine;     Show all 6 Subjects
Abstract:
... Leucine rich repeats (LRRs) occurring in tandem are 20–29 amino acids long. Eleven LRR types have been recognized. Sequence features of LRRs from viruses were investigated using over 600 LRR proteins from 89 species. Directly before, metagenome data of nucleo-cytoplasmic large dsDNA viruses (NCLDVs) have been published; the 2,074 NCLDVs encode 199,021 proteins. From the NCLDVs 547 LRR proteins wer ...
DOI:
10.1016/j.gene.2021.146156

20. PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data

Author:
Emilio Mastriani; Kathrina Mae Bienes; Gary Wong; Nicolas Berthet
Source:
Viruses 2022 v.14 no.6 pp. -
ISSN:
1999-4915
Subject:
metagenomics,   etc   ; Internet; computer software; nanopores; scientists;     Show all 5 Subjects
Abstract:
... The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and tim ...
DOI:
10.3390/v14061260