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Biological observations in microbiota analysis are robust to the choice of 16S rRNA gene sequencing processing algorithm: case study on human milk microbiota
BackgroundIn recent years, the microbiome field has undergone a shift from clustering-based methods of operational taxonomic unit (OTU) designation...
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Building Feature Table and Feature Representative Sequences from Raw Reads
Bioinformatic techniques have advanced to correct sequencing errors to determine real biological sequences at single nucleotide resolution by...
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Metagenomic Data Analysis
This volume describes different sequencing methods, pipelines and tools for metagenome data analyses. Chapters guide readers through quality control...
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The Direct Symbiotic Germination of Orchid Seeds in the Field
Mycorrhizal fungi are essential to the sustainability of the orchid population. Due to the minute nature of seeds, the mycobiont that the seedling...
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Delayed access to feed early post-hatch affects the development and maturation of gastrointestinal tract microbiota in broiler chickens
BackgroundThe first two weeks of post-hatch (PH) growth in broilers (meat-type birds) are critical for gut development and microbiota colonization....
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Vaginal microbiota in women with spontaneous preterm labor versus those with term labor in Kenya: a case control study
BackgroundPreterm birth is a global problem with about 12% of births in sub-Saharan Africa occurring before 37 weeks of gestation. Several studies...
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Analysis of gastric microbiome reveals three distinctive microbial communities associated with the occurrence of gastric cancer
BackgroundGastric microbial dysbiosis were reported to be associated with gastric cancer (GC). This study aimed to explore the variation, diversity,...
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Benchmark of 16S rRNA gene amplicon sequencing using Japanese gut microbiome data from the V1–V2 and V3–V4 primer sets
Background16S rRNA gene amplicon sequencing (16S analysis) is widely used to analyze microbiota with next-generation sequencing technologies. Here,...
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Assigning Taxonomy, Building Phylogenetic Tree
Taxonomic classification of the representative sequences and clustering of OTUs (Operational Taxonomic Units) are two core steps in bioinformatic...
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Phytobiome Metabarcoding: A Tool to Help Identify Prokaryotic and Eukaryotic Causal Agents of Undiagnosed Tree Diseases
Recent advancements in high-throughput sequencing have provided scientists with vastly enhanced tools to diagnose unknown tree diseases. One of these...
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Multivariate Longitudinal Microbiome Models
Chapter 15 mainly introduced the glmmTMB, GLMMadaptive, and FZINBMM packages. However, all these three packages...
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Basic Data Processing in QIIME 2
This chapter presents some basic data processing in QIIME 2. First it introduces importing and exporting data. Then it introduces extracting data...
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Unveiling microbial community structure in Ragi tape as elicitors to increase secondary metabolites contents in Glycine max and Vigna radiata
Previously, elicitation using microbe consortium inside Ragi Tape (RT) has given some insight with better results than mono-starter elicitation....
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Full Shotgun DNA Metagenomics
Full DNA metagenomics is the sequencing of all DNA from a sample followed by assembly and annotation and assignment of sequence information to...
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Comparative fungal diversity and dynamics in plant compartments at different developmental stages under root-zone restricted grapevines
BackgroundThe root-zone restriction cultivation technique is used to achieve superior fruit quality at the cost of limited vegetative and enhanced...
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Bacterial community dynamics during embryonic development of the little skate (Leucoraja erinacea)
BackgroundMicrobial transmission from parent to offspring is hypothesized to be widespread in vertebrates. However, evidence for this is limited as...
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Gut Metagenomic Profiling of Gossypol Induced Oxycarenus laetus (Hemiptera: Lygaeidae) Reveals Gossypol Tolerating Bacterial Species
Oxycarenus laetus is a cotton pest that primarily feeds on seeds that are rich in gossypol. Though gossypol is toxic to general herbivores, O. laetus ...
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Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome
BackgroundTargeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target...
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Computational Analysis of HTS Data and Its Application in Plant Pathology
High-throughput sequencing is a basic tool of biological research, and it is extensively used in plant pathology projects. Here, we describe how to...
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Study on the diversity of epiphytic bacteria on corn and alfalfa using Illumina MiSeq/NovaSeq high-throughput sequencing system
PurposeTo investigate the diversity of the epiphytic bacteria on corn ( Zea mays ) and alfalfa ( Medicago sativa ) collected in Hengshui City and...
