Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

Wang, Yulin; Niu, Qigui; Zhang, Xu; Liu, Lei; Wang, Yübo; Chen, Yiqiang; Negi, Mishty; Figeys, Daniel; Li, Yu You; Zhang, Tong

doi:10.1186/s40168-019-0730-6

Cited by 77 publications

(52 citation statements)

References 78 publications

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“…Besides, the IHA approach resulted in significantly more contiguous MAGs than the SR-based method (paired sample t test, P < 0.001). Thus, this highlighted the significance of hybrid assembly in the extension of highly fragmented contigs that are ubiquitous in SRs-based assembly and binning processes [ 14 , 15 , 53 – 56 ]. Furthermore, these results showcased that the IHA workflow can also retrieve MAGs with a very low relative abundance.…”

Section: Resultsmentioning

confidence: 99%

“…Both approaches showed concordance with each other, suggesting that the genome-based taxonomic assignments were sufficient to cover the MAG lineages within the PNA system. Microorganisms belonging to the phyla Bacteroidota , Chloroflexota , Proteobacteria , and Planctomycetota are always identified in anammox-related ecosystems [ 13 – 15 , 68 ]. The newly recovered (near-) complete MAGs will contribute to a further characterization of the bacterial repertoire of anammox-associated systems, as well as microbial ecology studies integrated with other technologies.…”

Section: Resultsmentioning

confidence: 99%

“…One sludge sample was collected on November 15, 2018, from a well-operated one-stage PNA reactor under the same operating parameters as in our previous study [ 15 ]. Genomic DNA was extracted using the DNeasy PowerSoil Kit (Qiagen, Hilden, Germany) according to the manufacturer’s instructions.…”

Section: Methodsmentioning

confidence: 99%

“…This may limit the ability to profile a full-picture of the microbial metabolic functions in relevant studies [ 11 , 12 ]. Currently, the complete genomes pertaining to anammox systems are very limited and most genomes are highly fragmented, rendering a more comprehensive understanding of the microbial community not feasible to be characterized [ 13 – 15 ].…”

Section: Introductionmentioning

confidence: 99%

“…1 ) proposed in this study to reconstruct high-quality and high-contiguity (HQ-HC) MAGs from a PNA dataset containing 111 gigabase pairs (Gbp) Illumina and 69 Gbp Nanopore reads. The resulting high-quality MAGs served as a valuable reference and enhanced earlier investigations of this anammox ecosystem by providing a more comprehensive gene inventory and genome structure of the contained organisms [ 15 ]. The genome retrieval performance of IHA workflow showcased that this approach could be used to produce a high-resolution profile of the microbial community composition and genome structure of other enrichment systems.…”

Section: Introductionmentioning

confidence: 99%

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High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

et al. 2020

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Background Genome-centric approaches are widely used to investigate microbial compositions, dynamics, ecology, and interactions within various environmental systems. Hundreds or even thousands of genomes could be retrieved in a single study contributed by the cost-effective short-read sequencing and developed assembly/binning pipelines. However, conventional binning methods usually yield highly fragmented draft genomes that limit our ability to comprehensively understand these microbial communities. Thus, to leverage advantage of both the long and short reads to retrieve more complete genomes from environmental samples is a must-do task to move this direction forward. Results Here, we used an iterative hybrid assembly (IHA) approach to reconstruct 49 metagenome-assembled genomes (MAGs), including 27 high-quality (HQ) and high-contiguity (HC) genomes with contig number ≤ 5, eight of which were circular finished genomes from a partial-nitritation anammox (PNA) reactor. These 49 recovered MAGs (43 MAGs encoding full-length rRNA, average N50 of 2.2 Mbp), represented the majority (92.3%) of the bacterial community. Moreover, the workflow retrieved HQ and HC MAGs even with an extremely low coverage (relative abundance < 0.1%). Among them, 34 MAGs could not be assigned to the genus level, indicating the novelty of the genomes retrieved using the IHA method proposed in this study. Comparative analysis of HQ MAG pairs reconstructed using two methods, i.e., hybrid and short reads only, revealed that identical genes in the MAG pairs represented 87.5% and 95.5% of the total gene inventory of hybrid and short reads only assembled MAGs, respectively. In addition, the first finished anammox genome of the genus Ca. Brocadia reconstructed revealed that there were two identical hydrazine synthase (hzs) genes, providing the exact gene copy number of this crucial phylomarker of anammox at the genome level. Conclusions Our results showcased the high-quality and high-contiguity genome retrieval performance and demonstrated the feasibility of complete genome reconstruction using the IHA workflow from the enrichment system. These (near-) complete genomes provided a high resolution of the microbial community, which might help to understand the bacterial repertoire of anammox-associated systems. Combined with other validation experiments, the workflow can enable a detailed view of the anammox or other similar enrichment systems.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

et al. 2020

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Effects of Docetaxel Injection and Docetaxel Micelles on the Intestinal Barrier and Intestinal Microbiota

Liu

Xiao

et al. 2021

Advanced Science

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Increasing evidence has suggested that chemotherapeutics affect the integrity of the intestinal barrier and alter the intestinal microbiota, thus limiting the therapeutic outcomes of cancer chemotherapy. Docetaxel (DTX) is used for breast cancer treatment and has gastrointestinal side effects, but the influence of DTX formulations on the intestinal barrier and intestinal microbiota remains unknown. Therefore, in this work, the influence of DTX injection (free DTX, commercial formulation) and DTX/methoxy poly(ethylene glycol)-block-poly(D,L-lactide) (mPEG-PDLLA) (DTX micelles, nanoformulation) on the integrity of the intestinal barrier and the intestinal microbiota is investigated. It is found that the free DTX causes significantly greater intestinal barrier damage than the DTX micelles. The diversity of the intestinal microbiota, and the relative abundance of Akkermansia muciniphila and Ruminococcus gnavus in the DTX micelle-treated group is significantly higher than that in the free DTX-treated group. Moreover, the tumor growth rate is elevated in antibiotic mixture-pretreated mice, demonstrating that the diversity and composition of the intestinal microbiota may be associated with tumor progression. This work demonstrates that different formulations of chemotherapeutics have different effects on the integrity of the intestinal barrier and the intestinal microbiota.

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Targeted metagenomics reveals extensive diversity of the denitrifying community in partial nitritation anammox and activated sludge systems

Orschler

Agrawal

Lackner

2020

Biotech & Bioengineering

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The substantial presence of denitrifiers has already been reported in partial nitritation anammox (PNA) systems using the 16S ribosomal RNA (rRNA) gene, but little is known about the phylogenetic diversity based on denitrification pathway functional genes. Therefore, we performed a metagenomic analysis to determine the distribution of denitrification genes and the associated phylogeny in PNA systems and whether a niche separation between PNA and conventional activated sludge (AS) systems exists. The results revealed a distinct abundance pattern of denitrification pathway genes and their association to the microbial species between PNA and AS systems. In contrast, the taxonomic analysis, based on the 16S rRNA gene, did not detect notable variability in denitrifying community composition across samples. In general, narG and nosZa2 genes were dominant in all samples. While the potential for different stages of denitrification was redundant, variation in species composition and lack of the complete denitrification gene pool in each species appears to confer niche separation between PNA and AS systems. This study suggests that targeted metagenomics can help to determine the denitrifying microbial composition at a fine-scale resolution while overcoming current biases in quantitative polymerase chain reaction approaches due to a lack of appropriate primers.

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Exploring the effects of operational mode and microbial interactions on bacterial community assembly in a one-stage partial-nitritation anammox reactor using integrated multi-omics

Cited by 77 publications

References 78 publications

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

High-quality bacterial genomes of a partial-nitritation/anammox system by an iterative hybrid assembly method

Effects of Docetaxel Injection and Docetaxel Micelles on the Intestinal Barrier and Intestinal Microbiota

Targeted metagenomics reveals extensive diversity of the denitrifying community in partial nitritation anammox and activated sludge systems

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