Literature Collection
Sample Preparation (Wet-Lab)
A noninvasive, cost- and time-effective alternative method to actively filter DNA from water samples.
Bessey et al. (2021) Passive eDNA collection enhances aquatic biodiversity analysis. Communication Biology, 4:236.
PCR inhibitors can originate from different sources like the source of the sample, extraction method or even from the plastics used during sample preparation.
Schrader et al. (2012) PCR inhibitors – occurrence, properties and removal. Journal of Applied Microbiology 113, 1014-1026
Synthetic spike-ins to improve the reliability and accuracy of AmpSeq microbiome studies.
Tourlousse et al. (2017) Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing, Nucleic Acids Research, 45-4.
LoopSeq, a commercially available synthetic long-read (SLR) sequencing technology for Illumina short-read sequencing platform.
Callahan et al. (2021) Ultra-accurate microbial amplicon sequencing with synthetic long reads. Microbiome 9:130
The flagellin gene (fliC) as a single-copy gene alternative to 16S AmpSeq.
Hu et al. (2022) Single-gene long-read sequencing illuminates Escherichia coli strain dynamics in the human intestinal microbiome. Cell Reports 38.
Annotation
A conceptual framework for the identification of fungi.
Lücking et al. (2020) Unambiguous identification of fungi: where do we stand and how accurate and precise is fungal DNA barcoding?. IMA Fungus 11: 14.
Data Analysis
A critique of the rapid growth of interest in microbiota research, highlighting concerns about oversimplification, misinterpretation and the need for real expertise in the field.
Boers et al. (2016) Suddenly everyone is a microbiota specialist. Clinical Microbiology and Infection 22(7):581-582.
A discussion about different approaches to define a core microbiome.
Neu et al. (2021) Defining and quantifying the core microbiome: Challenges and prospects. PNAS Vol. 118 No. 51.
The paper discusses how rarefaction is the most effective method for addressing sequencing depth variability in amplicon sequencing, offering better statistical power and accuracy compared to alternative techniques.
Schloss (2024) Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. mSphere 9(2).