High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils

Lewis, Ricky W.; Islam, Anjuman A.; Dilla-Ermita, Christine Jade; Hulbert, Scot H.; Sullivan, Tarah S.

doi:10.3791/59137

Cited by 5 publications

(3 citation statements)

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“…Overall, high-throughput sequencing approaches are currently the most predominant techniques to investigate microbiomes, in clinical research as well as in environmental science [42,43]. The recent developments in DNA sequencing technologies, also referred to as nextgeneration sequencing (NGS), now allow researchers to study complex biological samples based on sequence information on a large scale [44].…”

Section: How To Study Microbial Communities: Techniques Currently Avamentioning

confidence: 99%

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

et al. 2019

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Understanding the complex interactions of microbial communities including bacteria, archaea, parasites, viruses and fungi of the gastrointestinal tract (GIT) associated with states of either health or disease is still an expanding research field in both, human and veterinary medicine. GIT disorders and their consequences are among the most important diseases of domesticated Equidae, but current gaps of knowledge hinder adequate progress with respect to disease prevention and microbiome-based interventions. Current literature on enteral microbiomes mirrors a vast data and knowledge imbalance, with only few studies tackling archaea, viruses and eukaryotes compared with those addressing the bacterial components. Until recently, culture-dependent methods were used for the identification and description of compositional changes of enteral microorganisms, limiting the outcome to cultivatable bacteria only. Today, next generation sequencing technologies provide access to the entirety of genes (microbiome) associated with the microorganisms of the equine GIT including the mass of uncultured microbiota, or "microbial dark matter". This review illustrates methods commonly used for enteral microbiome analysis in horses and summarizes key findings reached for bacteria, viruses and fungi so far. Moreover, reasonable possibilities to combine different explorative techniques are described. As a future perspective, knowledge expansion concerning beneficial compositions of microorganisms within the equine GIT creates novel possibilities for early disorder diagnostics as well as innovative therapeutic approaches. In addition, analysis of shotgun metagenomic data enables tracking of certain microorganisms beyond species barriers: transmission events of bacteria including pathogens and opportunists harboring antibiotic resistance factors between different horses but also between humans and horses will reach new levels of depth concerning strain-level distinctions.

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Section: How To Study Microbial Communities: Techniques Currently Avamentioning

confidence: 99%

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

et al. 2019

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“…The microbiota composition in horse gut has been partly characterized based mainly on 16S amplicon sequencing [ 9 – 15 ], Recently, a gene catalogue and hundreds of MAG of horse gut microbiome have been reported [ 6 , 20 , 21 ], but large-scale studies on microbiota composition and function in horses are still lacking. The emergence of high-throughput sequencing and metagenome binning technology has made it possible to obtain nearly complete metagenome-assembled genomes (MAG) on a large scale [ 22 ]. Metagenomic sequencing technology can identify a large number of previously unknown bacterial species among intestinal microbes and has been used to characterize the functions of these microbes at the genomic level [ 22 – 26 ].…”

Section: Introductionmentioning

confidence: 99%

“…The emergence of high-throughput sequencing and metagenome binning technology has made it possible to obtain nearly complete metagenome-assembled genomes (MAG) on a large scale [ 22 ]. Metagenomic sequencing technology can identify a large number of previously unknown bacterial species among intestinal microbes and has been used to characterize the functions of these microbes at the genomic level [ 22 – 26 ]. This technology has generated thousands of MAG from humans [ 23 ], ruminants [ 24 ], chickens [ 25 ], pigs [ 26 ], and horse [ 6 ].…”

Section: Introductionmentioning

confidence: 99%

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse

Guo

et al. 2023

Microbiome

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Background As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses. Results Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance. Conclusion Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome.

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Buffer-free CAS assay using a diluted growth medium efficiently detects siderophore production and microbial growth

Murakami,

Tanaka,

Sato

et al. 2023

Biometals

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High-throughput Siderophore Screening from Environmental Samples: Plant Tissues, Bulk Soils, and Rhizosphere Soils

Cited by 5 publications

References 0 publications

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

The gut microbiome of horses: current research on equine enteral microbiota and future perspectives

Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse

Buffer-free CAS assay using a diluted growth medium efficiently detects siderophore production and microbial growth

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