Quantitative microbiome profiling reveals the developmental trajectory of the chicken gut microbiota and its connection to host metabolism

iMeta, Journal Year: 2023, Volume and Issue: 2(2)

Published: April 25, 2023

Abstract Revealing the assembly and succession of chicken gut microbiota is critical for a better understanding its role in physiology metabolism. However, few studies have examined dynamic changes absolute microbes using quantitative microbiome profiling (QMP) method. Here, we revealed developmental trajectory broiler bacteriome mycobiome by combining high‐throughput sequencing with microbial load quantification assay. We showed that abundance diversity reached plateau at 7 days posthatch (DPH), forming segment‐specific community types after 1 DPH. The was more impacted deterministic processes, affected stochastic processes. also observed stage‐specific different segments, three occurrence patterns including “colonization,” “disappearance,” “core” were defined. co‐occurrence networks very among positive associations than negative associations. Furthermore, provided links between their serum metabolite variations. Time‐course untargeted metabolomics six clusters changing abundance. foregut had connections metabolites, closely related to lipid amino acid present study full landscape development manner, metabolites further highlight impact growth development.

Language: Английский

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Duck gut metagenome reveals the microbiome signatures linked to intestinal regional, temporal development, and rearing condition

iMeta, Journal Year: 2024, Volume and Issue: 3(4)

Published: May 14, 2024

Abstract The duck gastrointestinal tract (GIT) harbors an abundance of microorganisms that play important role in health and production. Here, we constructed the first relatively comprehensive gut microbial gene catalog (24 million genes) 4437 metagenome‐assembled genomes using 375 GIT metagenomic samples from four different breeds across five intestinal segments under two distinct rearing conditions. We further characterized region‐specific taxonomy their assigned functions, as well temporal development maturation microbiome. Our analysis revealed similarity within microbiota foregut hindgut compartments, but distinctive taxonomic functional differences between segments. In addition, found a significant shift composition newly hatched ducks (3 days), followed by increased diversity enhanced stability growth stages (14, 42, 70 indicating develops into mature stable community host matures. Comparing impact conditions (with without water) on cecal communities bacterial capacity for lipopolysaccharide biosynthesis was significantly had free access to water, leading accumulation pathogenic bacteria antibiotic‐resistance genes. Taken together, our findings expand understanding microbiome signatures linked regional, development, ducks, which highlight poultry

Language: Английский

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Layer chicken microbiota: a comprehensive analysis of spatial and temporal dynamics across all major gut sections

Journal of Animal Science and Biotechnology/Journal of animal science and biotechnology, Journal Year: 2024, Volume and Issue: 15(1)

Published: Feb. 5, 2024

The gut microbiota influences chicken health, welfare, and productivity. A diverse balanced has been associated with improved growth, efficient feed utilisation, a well-developed immune system, disease resistance, stress tolerance in chickens. Previous studies on have predominantly focused broiler chickens usually limited to one or two sections of the digestive under controlled research environments, often sampled at single time point. To extend these studies, this investigation examined commercially raised layer across all major system regular sampling from rearing end production 80 weeks. aim was build detailed picture development entire study spatial temporal dynamics.

Language: Английский

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Unveiling the Kadaknath Gut Microbiome: Early Growth Phase Spatiotemporal Diversity

Microbiology Research, Journal Year: 2025, Volume and Issue: 16(3), P. 54 - 54

Published: Feb. 26, 2025

The early growth phase is a critical period for the development of chicken gut microbiome. In this study, spatiotemporal diversity gastrointestinal microbiota, shifts in taxonomic composition, and relative abundances main bacterial taxa were characterized Kadaknath, high-value indigenous Indian breed, using sequencing V3–V4 region 16S rRNA gene. To assess microbiome composition abundance shifts, three chickens per (3, 28, 35 days) sampled, with microbiota analyzed from regions (crop, small intestine, ceca) bird. results revealed Firmicutes as most abundant phylum Lactobacillus dominant genus across all stages. was particularly crop at stages (3 28 days), while ceca exhibited transition towards dominance Phocaeicola by day 35. Microbial richness evenness increased age, reflecting maturation, analyses microbial community distinct differences, on showing highest differentiation. Pathogen analysis highlighted peak poultry-associated Campylobacter, Staphylococcus, Clostridium paraputrificum 3-day-old underscoring vulnerability These findings provide insights into age-specific life-stage susceptibility to pathogens, emphasizing need targeted interventions optimize poultry health management performance.

Language: Английский

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ChatGPT and generative AI are revolutionizing the scientific community: A Janus‐faced conundrum

iMeta, Journal Year: 2024, Volume and Issue: 3(2)

Published: Feb. 27, 2024

The advent of generative artificial intelligence (AI) technologies marks a transformative moment for the scientific sphere, unlocking novel avenues to elevate writing's efficiency and quality, expedite insight discovery, enhance code development processes. Essential leveraging these advancements is prompt engineering, method that enhances AI interaction quality. Despite its benefits, effective application requires blending researchers' expertise with AI, avoiding overreliance. A balanced strategy integrating independent critical thinking ensures advancement quality research, innovation while maintaining research integrity. Since launch chatbot ChatGPT by OpenAl (November 2022), (Al) using large language models (LLMs) has increasingly penetrated community. survey reported in February 2023 revealed 80% respondents use chatbots [1]. By October 2023, about 30% postdocs were employing tasks like text refinement, generation, editing, literature management their fields [2]. end "Nature" journal recognized as one 10 pivotal contributors science year. In biomedical revolutionizing drug discovery predicting molecular structures biological interactions [3]. It also instrumental environmental science, simulating complex climate systems aid weather prediction change impact assessment [4]. Overall, are equipping scientists advanced tools processing extensive data, discerning patterns, uncovering insights might otherwise be overlooked. opened new horizons Generative markedly various aspects prime focus on improving review analysis. swiftly screening summarizing vast volumes literature, provide researchers essential background information emerging trends, thereby saving time enriching depth breadth. AI's contribution enhancing writing noteworthy. Leveraging natural processing, they editors drafting, proofreading, formatting, particularly beneficial nonnative English speakers crafting precise academic English. These efficiently organize format data theories, streamlining communication greater accuracy efficacy. aiding analyses evaluation. excel at analyzing datasets, revealing intricate correlations, anomalies elude human detection. This areas genomics, epidemiology, which involve large-scale can create snippets from user descriptions, translating into functional programming languages [5]. especially novices or those unfamiliar languages. Moreover, identifying correcting errors code, quickly pinpointing syntactical logical issues, providing explanations, accelerating debugging serving an educational resource developers. Additionally, maintainability, suggesting refactoring improve readability performance, line software best practices. interdisciplinary collaboration brainstorming offering suggestions, analogies, examples disciplines. approach broadens scope ideas, encourages beyond conventional boundaries, fosters creative problem-solving, crucial thrive innovation. diverse perspectives unexpected connections, challenge encourage problem-solving. similar significantly how communicate public, spread comprehension knowledge. They simplify content more accessible language, overcoming jargon barrier often alienates general public. Correspondingly, virtual persona designed iMETA journal, tasked summarizing, condensing, presenting articles, thus dissemination outreach. could even analyze substituting authors engaging readers. demystifies making it approachable. translation, plays key role bridging gaps communication, ensuring global accessibility, fostering inclusive discourse. Prompt engineering technique optimizing (Figure 1A). process entails not just instructing task hand, but formulating requests maximize output Effective involves selecting relevant keywords, adequate context, clearly defining objectives expectations. tailoring prompts model's specific capabilities constraints performance. Herein, we concise guide boost efficiency. Role-playing occupies distinct fascinating niche engineering. users emulating characters scenarios, drawing out imaginative contextually detailed responses. For instance, may adopt biochemist, microbiologist, bioinformatician, frame inquiries within narrative context. specificity certain problems techniques effectiveness role-playing scenarios 1Aa). essence this lies steering toward responses transcend standard, direct answers, deeper nuanced engagement. prompt, clarity instructions eliciting specific, relevant, high-quality outputs AI. Well-defined reduce ambiguity, response accuracy. strategies encompass specificity, contextual information, clear parameters, straightforward instruction structure prevent misunderstandings. microbiology genomics 1Ab), there marked progression highly prompts. shift highlights guidance, focused comprehensive research. methodical only streamlines optimizes experience conserves resources, efficient rewarding. Incorporating reference texts specialized subjects. enriches understanding, leading outputs. Reference materials mirroring tones styles, consistency established norms technical vernacular. example, when chicken microbiome, utilizing study (10.1002/imt2.105) improves [6]. be: "Using attached paper, write 500-word overview microbiome." Such directive leverages metagenomics yielding informed accurate summary 1Ac). Integrating external AI-generated expanding capabilities. Tools analysis visualization complement inherent functions, enabling richer interpret standalone capacity. synergy widens achievable spectrum heightens precision outcomes. assessing drug's blood pressure, patient pre- post-medication analyzed. Employing Python's SciPy paired t test determines statistical significance pressure changes. Subsequently, aided prompts, used alongside Python draw definitive conclusions effect 1Ad). final two principles AI-driven "systematically testing changes" "allowing model time." Systematic variation parameters outcome documentation optimal configurations. iterative fine-tuning settings careful comparison outcomes achieve linear logistic regression conducting omics 1Ae). Conversely, allocating sufficient vital tasks, permitting thoroughly handle datasets conduct analyses, considered results. Specific indicating extended 1Af), such "allow extra time" "allocate additional in-depth processing," instruct undertake thorough examination across including analysis, interpretation, While offers considerable advantages community, usage presents potential drawbacks, encompassing reliability ethical responsibility concerns. Diligent mitigate issues. primary concern data. 66% wary inaccuracies infiltrating papers [7]. models, trained existing sets, propagate outdated, biased, incomplete impacting output's relevance sake commercial advantages, architecture, training scale most publicly disclosed. When plugins, inputting yield However, lacking proper methodologies struggle discern correctness methods determine if occurred during process. imperative rigorously evaluate against authoritative sources, contexts. should function auxiliary tool augmenting rather than replacing expertise. preliminary idea draft creation, ultimate integrity rests experts. Data bias other poses significant challenge, develop generation interpretation based datasets. Inherently biased characterized stereotypes, prejudices, skewed representations, lead perpetuating biases consistently associates concepts groups, reinforce biases, deepening prejudices. critically assess outputs, findings interpretation. necessitates vigilance cross-verification impartial sources. Furthermore, educating community propensity imperative. Heightened awareness promotes prudent utilization originality publication paramount. excels synthesizing ability generate limited though adept unseen patterns sets. raises concerns plagiarism, 68% plagiarism complicate detection Although detectors being developed differentiate between [8], culture conduct. employed supplementary process, assisting review, ideation. core innovative contributions must stem researchers. require adaptation, work showcases unique modifies any content. issues due academia society. attributing authorship becomes complicated contributions. cannot credited co-authors [9], transparently acknowledged, acknowledgments section, preserve authorship. frequently retrieved uploaded ChatGPT, privacy security emerge, involved sensitive confidential. scenario risk unauthorized third-party access theft. include personal exacerbates challenges safeguarding breaches. Inaccurate unreliable pose misinformation dissemination. Therefore, establish follow guidelines frameworks address usage, bias, transparency, accountability. Excessive reliance undermine among researchers, education training. tools, rapid inadvertently accept solutions uncritically. diminish problem-solving skills weaken over time. To counter this, students educated scrutinize question AI-provided recognizing source. contexts, complement, replace, traditional learning methods, integration. Essentially, serves valuable exploring solutions, learners cultivate trust own skills. misuse multitude risks, malware, phishing, fraud, necessitating robust regulatory abuse. Enhancing public along government legal entities, developing curb illegal use. high energy demands operation raise Addressing algorithms, renewable computing centers, promoting footprint sustainable employment, reducing labor needs, calls human-machine collaboration. Supporting workforce transitions continuous adapting technological advancements. Interdisciplinary needed fully understand market inform policy recommendations. light discussions our editorial office journals [10], propose scholarly publishing. First, AI-assisted technologies, chatbots, authors. manuscript preparation Detailed used, versions, required submissions. Researchers ensure fairness content, bearing work's Manuscripts rejection improper use, prohibited. Generally, images multimedia accepted unless specifically allowed. Compliance protection laws mandatory copyright intellectual property surrounding considered. Human oversight always prevail decision-making. Finally, given evolution, stance AI-created adapt changing industry standards. Janus, dual-faced Roman god symbolizing beginnings, aptly represents duality LLMs. As year broader technology, business, society, bring both benefits 1B Information: Figure S1). Scientists recognize risks measures them. introduce standardized operational aimed mitigating stemming levels users. initiative promote uniformity system plugin launched, will continuously monitor interactions. intended adherence practices supervisory report upon conclusion activities. mitigation exercising judgment synergize relying solely stringent compliance handling approach, combining skill development, enables leverage preserving Note: opinion described article author's understanding current stage Our depending Al future. 4.0 was grammar correction image generator 1B. Zhongji Pu, Baolei Jia, Chun-Lin Shi drafted paper. All have revised, read, approved publication. supported grants Xianghu Laboratory (grant ID: 2023C4S01002), Key Scientific Research Plan Project Hangzhou (2023SZD0130), National Natural Science Foundation China (U23A20148), Agricultural Technology Innovation Program (CAAS-ZDRW202308). Jia associate editor iMeta. Canhui Lan Yong-Xin Liu Executive Editors Che Ok Jeon member iMeta board. Shuang-Jiang Jingyuan Fu Editors-in-Chief declared no competing interests. supports available Information article. Please note: publisher responsible functionality supporting supplied Any queries (other missing content) directed corresponding author

Language: Английский

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The multi-kingdom microbiome catalog of the chicken gastrointestinal tract

Biosafety and Health, Journal Year: 2024, Volume and Issue: 6(2), P. 101 - 115

Published: March 2, 2024

Chicken is an important food animal worldwide and plays role in human life by providing meat eggs. Despite recent significant advances gut microbiome studies, a comprehensive study of chicken bacterial, archaeal, viral genomes remains unavailable. In this study, we constructed multi-kingdom catalog (CMKMC), including 18,201 225 33,411 genomes, annotated over 6,076,006 protein-coding genes integrating 135 metagenomes publicly available metagenome-assembled (MAGs) from ten countries. We found that 812 240 MAGs our dataset were putative novel species genera, respectively, far beyond what was previously reported. The newly unclassified predominant Phyla Firmicutes_A (n = 263), followed Firmicutes 126), Bacteroidota 121), Proteobacteria 87). Most the classified species-level operational taxonomic units belong to Caudovirales. Approximately, 63.24 % viromes are predicted infect two or more hosts, complete circular viruses. Moreover, diverse auxiliary metabolic antibiotic resistance carried Together, CMKMC provides largest integrated date, functional insights into gastrointestinal tract microbiota, paves way for microbial interventions better health productivity.

Language: Английский

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iMetaOmics: Advancing human and environmental health through integrated meta‐omics

iMetaOmics., Journal Year: 2024, Volume and Issue: 1(1)

Published: Aug. 8, 2024

iMetaOmics is a quarterly international journal with the priority of publishing research work within scope One Health, featured well-designed omics. The also welcomes systematic integration extensive public datasets, new and meaningful perspectives, re-analysis high-impact data yielding different/valuable conclusions. microbiome plays critical roles in human [1], animal [2], plant nutrition health [3], food [4], environment [5], as well other aspects society (Figure 1). Metaomics, including metabarcoding, metagenomics, metatranscriptomics, metaproteomics, metabolomics, provide unique powerful tools to better understand taxonomy functions microbiome, biology, [6]. Aiming fill gap lacking top journals field Asia, iMeta Science Society its thousands Chinese scientist members found young but journal—iMeta (ISSN: 2770-5986; eISSN: 2770-596X). It has published more than 200 high-quality papers since 2022, original articles, reproducible methods protocols, systemic reviews peers updated novel findings, easy-to-use analytic tools, knowledge [7]. These publications include are not limited gut pertaining diseases [8], microbiota animals (e.g., chicken [9], pig [10], panda [11]), pan-cancer [12] pan-genome [13], soil associated diversity defense [14, 15], popular for metaomics analyses [16-18]. With great efforts contributions our stakeholders, like publisher, editorial board members, authors, reviewers, received first impact factor 23.7 2024, gradually accumulating broad diverse audiences readership, especially attracting explosive growth submissions recent days. To cope significantly increased submissions, we have from bimonthly journal. However, publication space maintaining high standard iMeta, still reject 90% although many them did an excellent work. Due success officially launching sister (eISSN: 2996-9514, ISSN: 2996-9506), further publish articles [19-23], [24-28], state-of-the-art methodologies [29, 30] satisfy increasing submission demand iMeta. Taking advantage same team, rejected manuscripts valuable/meaningful findings will be transferred iMetaOmics, together detailed comments reviewers. In this context, following review process shortened promote rapid publishing. Before official launch, 12 already been upon approval by authors issue. Currently, featuring reanalysis expected that establish reputation soon, attract wide range interest readers, contribute progress Human Environmental Health studies. Authors' own priority, while utilization analysis robust experimental validation can considered. Multiple evidence required support conclusion. New strategies advantage, indispensable. All used without reasonable concerns should publicly/temporally accessible reviewers editors. A video tutorial, software download, installation, operation, result displaying, highly recommended bioinformatic tools. Additionally, necessary ethics numbers, clear layouts, figures, significant expected. Chun-Lin Shi: Writing—original draft; writing—review editing. Tong Chen: Writing—review Canhui Lan: Ren-You Gan: Jun Yu: Fangqing Zhao: Yong-Xin Liu: editing; conceptualization. Zhao Yu hold position Editor-in-Chief iMetaOmics. Liu, Chen, Lan, Shi Gan Executive Editors

Language: Английский

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Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine

The Science of The Total Environment, Journal Year: 2023, Volume and Issue: 905, P. 167079 - 167079

Published: Sept. 14, 2023

Language: Английский

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Early fecal microbiota transplantation from high abdominal fat chickens affects recipient cecal microbiome and metabolism

Frontiers in Microbiology, Journal Year: 2024, Volume and Issue: 14

Published: Jan. 8, 2024

Abdominal fat deposition (AFD) in chickens is closely related to the gut microecological balance. In this study, microbiota from high-AFD was transplanted into same strain of 0-day-old chicks via fecal transplantation (FMT). The FTM with high AFD had no obvious effects on growth traits, adult body weight, carcass abdominal and percentage, but did reduce coefficient variation traits. FMT significantly decreased cecal microbiome richness, changed structure, regulated biological functions associated energy metabolism synthesis. Additionally, metabolite composition metabolic function recipient were also altered those controls. Transplantation chicken promoted fatty acid elongation biosynthesis reduced vitamins, steroids, carbohydrates cecum. These findings provide insights mechanisms by which affect host profiles deposition.

Language: Английский

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Bacterial load in meconium

iMeta, Journal Year: 2024, Volume and Issue: 3(1)

Published: Feb. 1, 2024

The spike-in plasmid method was utilized to perform an analysis on meconium and second-pass feces, yielding both relative absolute quantitative results. With the data, abundance of bacteria in 17 samples fecal were found be 1.14 × 10

Language: Английский

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