Microbial Community
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2022 ◽  
Vol 169 ◽  
pp. 104248
Qiong Liu ◽  
Cornelius Talade Atere ◽  
Zhenke Zhu ◽  
Muhammad Shahbaz ◽  
Xiaomeng Wei ◽  

Microbiome ◽  
2021 ◽  
Vol 9 (1) ◽  
Lei Liu ◽  
Yulin Wang ◽  
Yu Yang ◽  
Depeng Wang ◽  
Suk Hang Cheng ◽  

Abstract Background Long-read sequencing has shown its tremendous potential to address genome assembly challenges, e.g., achieving the first telomere-to-telomere assembly of a gapless human chromosome. However, many issues remain unresolved when leveraging error-prone long reads to characterize high-complexity metagenomes, for instance, complete/high-quality genome reconstruction from highly complex systems. Results Here, we developed an iterative haplotype-resolved hierarchical clustering-based hybrid assembly (HCBHA) approach that capitalizes on a hybrid (error-prone long reads and high-accuracy short reads) sequencing strategy to reconstruct (near-) complete genomes from highly complex metagenomes. Using the HCBHA approach, we first phase short and long reads from the highly complex metagenomic dataset into different candidate bacterial haplotypes, then perform hybrid assembly of each bacterial genome individually. We reconstructed 557 metagenome-assembled genomes (MAGs) with an average N50 of 574 Kb from a deeply sequenced, highly complex activated sludge (AS) metagenome. These high-contiguity MAGs contained 14 closed genomes and 111 high-quality (HQ) MAGs including full-length rRNA operons, which accounted for 61.1% of the microbial community. Leveraging the near-complete genomes, we also profiled the metabolic potential of the AS microbiome and identified 2153 biosynthetic gene clusters (BGCs) encoded within the recovered AS MAGs. Conclusion Our results established the feasibility of an iterative haplotype-resolved HCBHA approach to reconstruct (near-) complete genomes from highly complex ecosystems, providing new insights into “complete metagenomics”. The retrieved high-contiguity MAGs illustrated that various biosynthetic gene clusters (BGCs) were harbored in the AS microbiome. The high diversity of BGCs highlights the potential to discover new natural products biosynthesized by the AS microbial community, aside from the traditional function (e.g., organic carbon and nitrogen removal) in wastewater treatment.

2021 ◽  
Vol 12 ◽  
Changwoo Park ◽  
Seung Bum Kim ◽  
Sang Ho Choi ◽  
Seil Kim

Microbial community analysis based on the 16S rRNA-gene is used to investigate both beneficial and harmful microorganisms in various fields and environments. Recently, the next-generation sequencing (NGS) technology has enabled rapid and accurate microbial community analysis. Despite these advantages of NGS based metagenomics study, sample transport, storage conditions, amplification, library preparation kits, sequencing, and bioinformatics procedures can bias microbial community analysis results. In this study, eight mock communities were pooled from genomic DNA of Lactobacillus acidophilus KCTC 3164T, Limosilactobacillus fermentum KCTC 3112T, Lactobacillus gasseri KCTC 3163T, Lacticaseibacillus paracasei subsp. paracasei KCTC 3510T, Limosilactobacillus reuteri KCTC 3594T, Lactococcus lactis subsp. lactis KCTC 3769T, Bifidobacterium animalis subsp. lactis KCTC 5854T, and Bifidobacterium breve KCTC 3220T. The genomic DNAs were quantified by droplet digital PCR (ddPCR) and were mixed as mock communities. The mock communities were amplified with various 16S rRNA gene universal primer pairs and sequenced by MiSeq, IonTorrent, MGIseq-2000, Sequel II, and MinION NGS platforms. In a comparison of primer-dependent bias, the microbial profiles of V1-V2 and V3 regions were similar to the original ratio of the mock communities, while the microbial profiles of the V1-V3 region were relatively biased. In a comparison of platform-dependent bias, the sequence read from short-read platforms (MiSeq, IonTorrent, and MGIseq-2000) showed lower bias than that of long-read platforms (Sequel II and MinION). Meanwhile, the sequences read from Sequel II and MinION platforms were relatively biased in some mock communities. In the data of all NGS platforms and regions, L. acidophilus was greatly underrepresented while Lactococcus lactis subsp. lactis was generally overrepresented. In all samples of this study, the bias index (BI) was calculated and PCA was performed for comparison. The samples with biased relative abundance showed high BI values and were separated in the PCA results. In particular, analysis of regions rich in AT and GC poses problems for genome assembly, which can lead to sequencing bias. According to this comparative analysis, the development of reference material (RM) material has been proposed to calibrate the bias in microbiome analysis.

Healthcare ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1371
Luciana Caenazzo ◽  
Pamela Tozzo

In recent years many studies have highlighted the great potential of microbial analysis in human identification for forensic purposes, with important differences in microbial community composition and function across different people and locations, showing a certain degree of uncertainty. Therefore, further studies are necessary to enable forensic scientists to evaluate the risk of microbial transfer and recovery from various items and to further critically evaluate the suitability of current human DNA recovery protocols for human microbial profiling for identification purposes. While the establishment and development of microbiome research biobanks for clinical applications is already very structured, the development of studies on the applicability of microbiome biobanks for forensic purposes is still in its infancy. The creation of large population microbiome biobanks, specifically dedicated to forensic human identification, could be worthwhile. This could also be useful to increase the practical applications of forensic microbiology for identification purposes, given that this type of evidence is currently absent from most real casework investigations and judicial proceedings in courts.

2021 ◽  
pp. 1-11
Limin Wang ◽  
Dongfeng Huang

Microbes play vital roles in soil quality; however, their response to N (nitrogen) and P (phosphorus) fertilization in acidic paddy soils of subtropical China remains poorly understood. Here, a 10-year field experiment was conducted to evaluate the effects of different fertilization treatments on microbial communities by Illumina MiSeq sequencing. The results showed that different fertilization treatments did not exert a significant effect on microbial alpha diversity, but altered soil properties, and thus affected microbial community composition. The microbial communities in the T1 (optimized N and P fertilizer) and T2 (excessive N fertilizer) treated soils differed from those in the T0 (no N and P fertilizer) and T3 (excessive P fertilizer) treated soils. In addition, the bacterial phyla Proteobacteria, Chloroflexi, and Acidobacteria, and the fungal phyla Ascomycota and Basidiomycota dominated all the fertilized treatments. Soil total potassium (TK) concentration was the most important factor driving the variation in bacterial community structure under different fertilization regimes, while the major factors shaping fungal community structure were soil TN and NO3–-N (nitrate N). These findings indicate that optimization of N and P application rates might result in variations in soil properties, which changed the microbial community structure in the present study.

2021 ◽  
Vol 12 ◽  
Magali Ranchou-Peyruse ◽  
Marion Guignard ◽  
Franck Casteran ◽  
Maïder Abadie ◽  
Clémence Defois ◽  

Deep aquifers (up to 2km deep) contain massive volumes of water harboring large and diverse microbial communities at high pressure. Aquifers are home to microbial ecosystems that participate in physicochemical balances. These microorganisms can positively or negatively interfere with subsurface (i) energy storage (CH4 and H2), (ii) CO2 sequestration; and (iii) resource (water, rare metals) exploitation. The aquifer studied here (720m deep, 37°C, 88bar) is naturally oligotrophic, with a total organic carbon content of <1mg.L−1 and a phosphate content of 0.02mg.L−1. The influence of natural gas storage locally generates different pressures and formation water displacements, but it also releases organic molecules such as monoaromatic hydrocarbons at the gas/water interface. The hydrocarbon biodegradation ability of the indigenous microbial community was evaluated in this work. The in situ microbial community was dominated by sulfate-reducing (e.g., Sva0485 lineage, Thermodesulfovibriona, Desulfotomaculum, Desulfomonile, and Desulfovibrio), fermentative (e.g., Peptococcaceae SCADC1_2_3, Anaerolineae lineage and Pelotomaculum), and homoacetogenic bacteria (“Candidatus Acetothermia”) with a few archaeal representatives (e.g., Methanomassiliicoccaceae, Methanobacteriaceae, and members of the Bathyarcheia class), suggesting a role of H2 in microenvironment functioning. Monoaromatic hydrocarbon biodegradation is carried out by sulfate reducers and favored by concentrated biomass and slightly acidic conditions, which suggests that biodegradation should preferably occur in biofilms present on the surfaces of aquifer rock, rather than by planktonic bacteria. A simplified bacterial community, which was able to degrade monoaromatic hydrocarbons at atmospheric pressure over several months, was selected for incubation experiments at in situ pressure (i.e., 90bar). These showed that the abundance of various bacterial genera was altered, while taxonomic diversity was mostly unchanged. The candidate phylum Acetothermia was characteristic of the community incubated at 90bar. This work suggests that even if pressures on the order of 90bar do not seem to select for obligate piezophilic organisms, modifications of the thermodynamic equilibria could favor different microbial assemblages from those observed at atmospheric pressure.

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