Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick

Bogomolnaya, Lydia M.; Talamantes, Marissa; Rocha, Júlio César; Nagarajan, Aravindh; Zhu, Wenhan; Spiga, Luisella; Winter, Maria G.; Konganti, Kranti; Adams, L. Garry; Winter, Sebastian; Andrews‐Polymenis, Helene

doi:10.1128/mbio.02444-22

Cited by 2 publications

(3 citation statements)

References 59 publications

(66 reference statements)

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“…Metabolic pathway analysis of the cecal content from birds infected with SE revealed a disruption in microbiota metabolic pathways related to arginine and proline metabolism as well as reduced tricarboxylic acid cycle (TCA) activity. Similarly, ST infection of chick early post-hatch also found revealed differences with non-infected animals in metabolic composition of ceca content including lactate, the main product of glucose fermentation of Enterococcus [ 87 ], supporting the observation that enterococci are significant members of the cecal microbiota during Salmonella infection. Furthermore, the microbiota composition was unchanged in neonatal chicks infected with ST, but the functional activity of the microbiota was dramatically altered [ 86 ].…”

Section: Salmonella Interactions With the Intestinal Ecosyst...mentioning

confidence: 71%

“…Furthermore, the microbiota composition was unchanged in neonatal chicks infected with ST, but the functional activity of the microbiota was dramatically altered [ 86 ]. For example, ST infection induced the increase expression of genes involved in branched-chain amino acid (BCAA) production, such as leucine, isoleucine, and valine [ 86 ] which play a key role in the growth, production performance, immunity, and intestinal health of chickens [ 87 , 88 ].…”

Section: Salmonella Interactions With the Intestinal Ecosyst...mentioning

confidence: 99%

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Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

Kogut,

Fernandez Miyakawa

2023

Animals

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The gastrointestinal ecosystem involves interactions between the host, gut microbiota, and external environment. To colonize the gut of poultry, Salmonella must surmount barriers levied by the intestine including mucosal innate immune responses and microbiota-mediated niche restrictions. Accordingly, comprehending Salmonella intestinal colonization in poultry requires an understanding of how the pathogen interacts with the intestinal ecosystem. In chickens, the paratyphoid Salmonella have evolved the capacity to survive the initial immune response and persist in the avian ceca for months without triggering clinical signs. The persistence of a Salmonella infection in the avian host involves both host defenses and tolerogenic defense strategies. The initial phase of the Salmonella–gut ecosystem interaction is characteristically an innate pro-inflammatory response that controls bacterial invasion. The second phase is initiated by an expansion of the T regulatory cell population in the cecum of Salmonella-infected chickens accompanied by well-defined shifts in the enteric neuro-immunometabolic pathways that changes the local phenotype from pro-inflammatory to an anti-inflammatory environment. Thus, paratyphoid Salmonella in chickens have evolved a unique survival strategy that minimizes the inflammatory response (disease resistance) during the initial infection and then induces an immunometabolic reprogramming in the cecum that alters the host defense to disease tolerance that provides an environment conducive to drive asymptomatic carriage of the bacterial pathogen.

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Section: Salmonella Interactions With the Intestinal Ecosyst...mentioning

confidence: 71%

Section: Salmonella Interactions With the Intestinal Ecosyst...mentioning

confidence: 99%

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

Kogut,

Fernandez Miyakawa

2023

Animals

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“…The metabolic pathways, and the presence of virulence and antimicrobial resistance genes, can thus be investigated in a quali-quantitative manner [92]. Because of the extensive links among microbiota, microbiota metabolism, host physiology, productivity, and health, the investigation of microbial community changes after various treatments (e.g., diets, housing conditions, or administration of antimicrobial agents and probiotics, etc; Figure 2) can enable direct interventions that maximize animal welfare and farm profitability [93][94][95]. Another benefit of parallel sequencing capabilities is the ability to "read" the same region of the genome hundreds or thousands of times.…”

Section: Molecular Epidemiology Of Pathogensmentioning

confidence: 99%

When Everything Becomes Bigger: Big Data for Big Poultry Production

Franzo

Legnardi

Faustini

et al. 2023

Animals

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In future decades, the demand for poultry meat and eggs is predicted to considerably increase in pace with human population growth. Although this expansion clearly represents a remarkable opportunity for the sector, it conceals a multitude of challenges. Pollution and land erosion, competition for limited resources between animal and human nutrition, animal welfare concerns, limitations on the use of growth promoters and antimicrobial agents, and increasing risks and effects of animal infectious diseases and zoonoses are several topics that have received attention from authorities and the public. The increase in poultry production must be achieved mainly through optimization and increased efficiency. The increasing ability to generate large amounts of data (“big data”) is pervasive in both modern society and the farming industry. Information accessibility—coupled with the availability of tools and computational power to store, share, integrate, and analyze data with automatic and flexible algorithms—offers an unprecedented opportunity to develop tools to maximize farm profitability, reduce socio-environmental impacts, and increase animal and human health and welfare. A detailed description of all topics and applications of big data analysis in poultry farming would be infeasible. Therefore, the present work briefly reviews the application of sensor technologies, such as optical, acoustic, and wearable sensors, as well as infrared thermal imaging and optical flow, to poultry farming. The principles and benefits of advanced statistical techniques, such as machine learning and deep learning, and their use in developing effective and reliable classification and prediction models to benefit the farming system, are also discussed. Finally, recent progress in pathogen genome sequencing and analysis is discussed, highlighting practical applications in epidemiological tracking, and reconstruction of microorganisms’ population dynamics, evolution, and spread. The benefits of the objective evaluation of the effectiveness of applied control strategies are also considered. Although human-artificial intelligence collaborations in the livestock sector can be frightening because they require farmers and employees in the sector to adapt to new roles, challenges, and competencies—and because several unknowns, limitations, and open-ended questions are inevitable—their overall benefits appear to be far greater than their drawbacks. As more farms and companies connect to technology, artificial intelligence (AI) and sensing technologies will begin to play a greater role in identifying patterns and solutions to pressing problems in modern animal farming, thus providing remarkable production-based and commercial advantages. Moreover, the combination of diverse sources and types of data will also become fundamental for the development of predictive models able to anticipate, rather than merely detect, disease occurrence. The increasing availability of sensors, infrastructures, and tools for big data collection, storage, sharing, and analysis—together with the use of open standards and integration with pathogen molecular epidemiology—have the potential to address the major challenge of producing higher-quality, more healthful food on a larger scale in a more sustainable manner, thereby protecting ecosystems, preserving natural resources, and improving animal and human welfare and health.

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Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick

Cited by 2 publications

References 59 publications

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

Phenotype Alterations in the Cecal Ecosystem Involved in the Asymptomatic Intestinal Persistence of Paratyphoid Salmonella in Chickens

When Everything Becomes Bigger: Big Data for Big Poultry Production

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