Recent advanced technologies for the characterization of xenobiotic-degrading microorganisms and microbial communities

S Mishra, Z Lin, S Pang, W Zhang, P Bhatt… - … in Bioengineering and …, 2021 - frontiersin.org
Global environmental contamination with a complex mixture of xenobiotics has become a
major environmental issue worldwide. Many xenobiotic compounds severely impact the …

Perspectives and benefits of high-throughput long-read sequencing in microbial ecology

L Tedersoo, M Albertsen, S Anslan… - Applied and …, 2021 - Am Soc Microbiol
Short-read, high-throughput sequencing (HTS) methods have yielded numerous important
insights into microbial ecology and function. Yet, in many instances short-read HTS …

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis

JS Johnson, DJ Spakowicz, BY Hong… - Nature …, 2019 - nature.com
The 16S rRNA gene has been a mainstay of sequence-based bacterial analysis for
decades. However, high-throughput sequencing of the full gene has only recently become a …

High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution

BJ Callahan, J Wong, C Heiner, S Oh… - Nucleic acids …, 2019 - academic.oup.com
Targeted PCR amplification and high-throughput sequencing (amplicon sequencing) of 16S
rRNA gene fragments is widely used to profile microbial communities. New long-read …

The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies

J Pollock, L Glendinning, T Wisedchanwet… - Applied and …, 2018 - Am Soc Microbiol
The development and continuous improvement of high-throughput sequencing platforms
have stimulated interest in the study of complex microbial communities. Currently, the most …

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

SM Karst, RM Ziels, RH Kirkegaard, EA Sørensen… - Nature …, 2021 - nature.com
High-throughput amplicon sequencing of large genomic regions remains challenging for
short-read technologies. Here, we report a high-throughput amplicon sequencing approach …

The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology

J Jeong, K Yun, S Mun, WH Chung, SY Choi, Y Nam… - Scientific reports, 2021 - nature.com
Characterizing the microbial communities inhabiting specimens is one of the primary
objectives of microbiome studies. A short-read sequencing platform for reading partial …

PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives

L Tedersoo, A Tooming‐Klunderud… - New Phytologist, 2018 - Wiley Online Library
Second‐generation, high‐throughput sequencing methods have greatly improved our
understanding of the ecology of soil microorganisms, yet the short barcodes (< 500 bp) …

A Sequel to Sanger: amplicon sequencing that scales

PDN Hebert, TWA Braukmann, SWJ Prosser… - BMC genomics, 2018 - Springer
Background Although high-throughput sequencers (HTS) have largely displaced their
Sanger counterparts, the short read lengths and high error rates of most platforms constrain …

The meconium microbiota shares more features with the amniotic fluid microbiota than the maternal fecal and vaginal microbiota

Q He, LY Kwok, X Xi, Z Zhong, T Ma, H Xu, H Meng… - Gut …, 2020 - Taylor & Francis
The early-life gut microbiota is associated with potential development of diseases in
adulthood. The sterile womb paradigm has been challenged by recent reports that revealed …