Insights Into Culturomics of the Rumen Microbiome

Zehavi, Tamar; Probst, Maraike; Mizrahi, Itzhak

doi:10.3389/fmicb.2018.01999

Cited by 41 publications

(41 citation statements)

References 52 publications

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“…Comprehensive culturing, either involving taxon-specific or oligotrophic medium compositions, often permits access to diverse, rare prokaryotes not depicted by molecular techniques alone (Hardoim et al, 2014;Zehavi et al, 2018;Karimi et al, 2019;Rego et al, 2019) while enabling access to their metabolism and bioactivities. For instance, broad-spectrum antimicrobial activities have been reported for freshwater sponge-associated Pseudomonas spp.…”

Section: Genetic Diversity and Novelty -Bioprospecting Potentialmentioning

confidence: 99%

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential

2020

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Current research on the prokaryotic low abundance taxa, the prokaryotic rare biosphere, is growing, leading to a greater understanding of the mechanisms underlying organismal rarity and its relevance in ecology. From this emerging knowledge it is possible to envision innovative approaches in biotechnology applicable to several sectors. Bioremediation and bioprospecting are two of the most promising areas where such approaches could find feasible implementation, involving possible new solutions to the decontamination of polluted sites and to the discovery of novel gene variants and pathways based on the attributes of rare microbial communities. Bioremediation can be improved through the realization that diverse rare species can grow abundant and degrade different pollutants or possibly transfer useful genes. Further, most of the prokaryotic diversity found in virtually all environments belongs in the rare biosphere and remains uncultivatable, suggesting great bioprospecting potential within this vast and understudied genetic pool. This Mini Review argues that knowledge of the ecophysiology of rare prokaryotes can aid the development of future, efficient biotechnology-based processes, products and services. However, this promise may only be fulfilled through improvements in (and optimal blending of) advanced microbial culturing and physiology, metagenomics, genome annotation and editing, and synthetic biology, to name a few areas of relevance. In the future, it will be important to understand how activity profiles relate with abundance, as some rare taxa can remain rare and increase activity, whereas other taxa can grow abundant. The metabolic mechanisms behind those patterns can be useful in designing biotechnological processes.

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Section: Genetic Diversity and Novelty -Bioprospecting Potentialmentioning

confidence: 99%

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential

2020

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“…(1,012 out of 1,698) (29). This discrepancy may speak to the power of cultivation relative to the power of direct molecular analyses in describing the diversity of a community.…”

Section: Cultivation Yields Complex Datamentioning

confidence: 99%

“…The copyright holder for this preprint this version posted November 20, 2020. ; https://doi.org/10.1101/2020.11.19.390864 doi: bioRxiv preprint When cultivation approaches are coupled with molecular analyses, the total diversity and identity of cultivated taxa can be determined (26)(27)(28), and specific, targeted taxa can be detected (13). More recently, high throughput sequencing has made it possible to quantify exactly what proportion of the original sample has been cultivated (26,29,30). Studies using this approach showed that roughly 23% of microorganisms in bovine rumen fluid were cultivable in liquid enrichments (29), while 96% of those in human bronchoalveolar lavage samples (30), and 60% of those detected in/on American toads (26) were cultivated.…”

Section: Introductionmentioning

confidence: 99%

Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

Stevenson

2020

Preprint

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Molecular techniques continue to reveal a growing disparity between the immense diversity of microbial life and the small proportion that is in pure culture. The disparity, originally dubbed “the great plate count anomaly” by Staley and Konopka, has become even more vexing given our increased understanding of the importance of microbiomes to a host and the role of microorganisms in the vital biogeochemical functions of our biosphere. Searching for novel antimicrobial drug targets often focuses on screening a broad diversity of microorganisms. If diverse microorganisms are to be screened, they need to be cultivated. Recent innovative research has used molecular techniques to assess the efficacy of cultivation efforts, providing invaluable feedback to cultivation strategies for isolating targeted and/or novel microorganisms. Here, we aimed to determine the efficiency of cultivating representative microorganisms from a non-human, mammalian microbiome, identify those microorganisms, and determine the bioactivity of isolates. Molecular methods indicated that around 57% of the ASVs detected in the original inoculum were cultivated in our experiments, but nearly 53% of the total ASVs that were present in our cultivation experiments were not detected in the original inoculum. In light of our controls, our data suggests that when molecular tools were used to characterize our cultivation efforts, they provided a more complete, albeit more complex, understanding of which organisms were present compared to what was eventually cultivated. Lastly, about 3% of the isolates collected from our cultivation experiments showed inhibitory bioactivity against a multidrug-resistant pathogen panel, further highlighting the importance of informing and directing future cultivation efforts with molecular tools.ImportanceCultivation is the definitive tool to understand a microorganism’s physiology, metabolism, and ecological role(s). Despite continuous efforts to hone this skill, researchers are still observing yet-to-be cultivated organisms through high-throughput sequencing studies. Here, we use the very same tool that highlights biodiversity to assess cultivation efficiency. When applied to drug discovery, where screening a vast number of isolates for bioactive metabolites is common, cultivating redundant organisms is a hindrance. However, we observed that cultivating in combination with molecular tools can expand the observed diversity of an environment and its community, potentially increasing the number of microorganisms to be screened for natural products.

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“…Improvements in sequencing technologies have also provided new insights into ecological shifts that occur in the host microbiota after different dietary/treatment regiments [ 8 , 9 ]. Culturomics, a new field centered on cultivating ruminant microorganisms, utilizes NGS and is driven by understanding the biochemical potential of individual microbes [ 10 ].…”

Section: Introductionmentioning

confidence: 99%

Use of Integrative Interactomics for Improvement of Farm Animal Health and Welfare: An Example with Fescue Toxicosis

Mote

Filipov

2020

Toxins

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Rapid scientific advances are increasing our understanding of the way complex biological interactions integrate to maintain homeostatic balance and how seemingly small, localized perturbations can lead to systemic effects. The ‘omics movement, alongside increased throughput resulting from statistical and computational advances, has transformed our understanding of disease mechanisms and the multi-dimensional interaction between environmental stressors and host physiology through data integration into multi-dimensional analyses, i.e., integrative interactomics. This review focuses on the use of high-throughput technologies in farm animal research, including health- and toxicology-related papers. Although limited, we highlight recent animal agriculture-centered reports from the integrative multi-‘omics movement. We provide an example with fescue toxicosis, an economically costly disease affecting grazing livestock, and describe how integrative interactomics can be applied to a disease with a complex pathophysiology in the pursuit of novel treatment and management approaches. We outline how ‘omics techniques have been used thus far to understand fescue toxicosis pathophysiology, lay out a framework for the fescue toxicosis integrome, identify some challenges we foresee, and offer possible means for addressing these challenges. Finally, we briefly discuss how the example with fescue toxicosis could be used for other agriculturally important animal health and welfare problems.

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Insights Into Culturomics of the Rumen Microbiome

Cited by 41 publications

References 52 publications

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential

The Link Between the Ecology of the Prokaryotic Rare Biosphere and Its Biotechnological Potential

Assessing and Maximizing Cultivated Diversity with Plate-Wash PCR and High Throughput Sequencing

Use of Integrative Interactomics for Improvement of Farm Animal Health and Welfare: An Example with Fescue Toxicosis

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