Articoli di riviste: "Microbiome engineering"

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Jin Song, Se, Douglas C. Woodhams, Cameron Martino, Celeste Allaband, Andre Mu, Sandrine Javorschi-Miller-Montgomery, Jan S. Suchodolski e Rob Knight. "Engineering the microbiome for animal health and conservation". Experimental Biology and Medicine 244, n. 6 (18 febbraio 2019): 494–504. http://dx.doi.org/10.1177/1535370219830075.

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Interest in animal microbiomes as therapeutics is rapidly expanding, as techniques to study the microbial world decrease in cost and increase in accessibility and case studies from human medicine receive widespread attention. In this review, we summarize the current state of techniques to modify the microbiome to improve animal health, focusing on applications in domestic pets, farm animals, and in wild settings for conservation. We discuss options for modifying the microbiome, including community-wide changes such as fecal microbiota transplants, prebiotics, probiotics, and antibiotics, and more targeted approaches such as phage therapy and CRISPR-Cas. We conclude that although much remains to be done in untangling the basic biology of microbiome-directed therapies in animals, the rapid progress currently being made in human medicine and the examples to date of application of probiotics and other microbiome-directed therapies in taxa ranging from horses to salamanders to bees suggest excellent prospects for these technologies as they are further developed and as data on both the benefits and risks are carefully and systematically collected. Impact statement Considering the clear effects of microbiota on important aspects of animal biology and development (including in humans), this topic is timely and broadly appealing, as it compels us to consider the possibilities of altering the microbiome (without antibiotics) to positively affect animal health. In this review, we highlight three general approaches to manipulating the microbiome that have demonstrated success and promise for use in animal health. We also point out knowledge gaps where further inquiry would most benefit the field. Our paper not only provides a short and digestible overview of the current state of application, but also calls for further exploration of the microbial diversity at hand to expand our toolkit, while also leveraging the diversity and flexibility of animal systems to better understand mechanisms of efficacy.

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Sonnenburg, Justin L. "Microbiome Engineering". Nature 518, n. 7540 (febbraio 2015): S10. http://dx.doi.org/10.1038/518s10a.

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Sonnenburg, Justin L. "Microbiome Engineering". Scientific American 312, n. 3 (17 febbraio 2015): S10. http://dx.doi.org/10.1038/scientificamerican0315-s10.

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Khan, Saad, Ruth Hauptman e Libusha Kelly. "Engineering the Microbiome to Prevent Adverse Events: Challenges and Opportunities". Annual Review of Pharmacology and Toxicology 61, n. 1 (6 gennaio 2021): 159–79. http://dx.doi.org/10.1146/annurev-pharmtox-031620-031509.

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In the past decade of microbiome research, we have learned about numerous adverse interactions between the microbiome and medical interventions such as drugs, radiation, and surgery. What if we could alter our microbiomes to prevent these events? In this review, we discuss potential routes to mitigate microbiome adverse events, including applications from the emerging field of microbiome engineering. We highlight cases where the microbiome acts directly on a treatment, such as via differential drug metabolism, and cases where a treatment directly harms the microbiome, such as in radiation therapy. Understanding and preventing microbiome adverse events is a difficult challenge that will require a data-driven approach involving causal statistics, multiomics techniques, and a personalized means of mitigating adverse events. We propose research considerations to encourage productive work in preventing microbiome adverse events, and we highlight the many challenges and opportunities that await.

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Møller, Katrine V., Jonas Bruhn Wesseltoft, Richelle Malazarte, Sabrina J. Kousgaard, Hans L. Nielsen, Erika Yashiro e Anders Olsen. "Usage of Cultured Human Fecal Microbiota for Colonization of Caenorhabditis elegans to Study Host–Microbe Interaction". Applied Microbiology 3, n. 4 (28 settembre 2023): 1130–43. http://dx.doi.org/10.3390/applmicrobiol3040078.

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The role of the microbiota in health and disease is a research area receiving much attention in academia and industry. A person’s microbiota refers to a community of microorganisms found mainly in the gut. It is estimated that around 39 trillion bacteria can be found on and inside the human body and there is increasing evidence that they influence human health. Advances in sequencing techniques are revolutionizing characterization of the human microbiome. However, causality and underlying molecular mechanisms are still largely unknown due to the complexity of the human microbiome and its interaction with the host. Turning towards simpler host organisms and using well-defined microbiomes are two ways to strengthen studies of causality and mechanism. Here, we show that the nematode Caenorhabditis elegans can be used as host to study sub-microbiomes derived from human feces samples prepared for fecal microbiota transplantation following a simple feeding protocol. Approximately 200 amplicon sequence variants were identified in the worm gut following transplantation with human fecal microbiota samples. We find that the gut microbiome does not simply reflect the bacterial community initially fed to the worms. Hence, our experimental setup can be used to identify and characterize host genetic factors shaping the microbiota and improving our understanding of host–human microbiome interactions.

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Yang, Letao, Lin Y. Hung, Yuefei Zhu, Suwan Ding, Kara G. Margolis e Kam W. Leong. "Material Engineering in Gut Microbiome and Human Health". Research 2022 (21 luglio 2022): 1–32. http://dx.doi.org/10.34133/2022/9804014.

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Tremendous progress has been made in the past decade regarding our understanding of the gut microbiome’s role in human health. Currently, however, a comprehensive and focused review marrying the two distinct fields of gut microbiome and material research is lacking. To bridge the gap, the current paper discusses critical aspects of the rapidly emerging research topic of “material engineering in the gut microbiome and human health.” By engaging scientists with diverse backgrounds in biomaterials, gut-microbiome axis, neuroscience, synthetic biology, tissue engineering, and biosensing in a dialogue, our goal is to accelerate the development of research tools for gut microbiome research and the development of therapeutics that target the gut microbiome. For this purpose, state-of-the-art knowledge is presented here on biomaterial technologies that facilitate the study, analysis, and manipulation of the gut microbiome, including intestinal organoids, gut-on-chip models, hydrogels for spatial mapping of gut microbiome compositions, microbiome biosensors, and oral bacteria delivery systems. In addition, a discussion is provided regarding the microbiome-gut-brain axis and the critical roles that biomaterials can play to investigate and regulate the axis. Lastly, perspectives are provided regarding future directions on how to develop and use novel biomaterials in gut microbiome research, as well as essential regulatory rules in clinical translation. In this way, we hope to inspire research into future biomaterial technologies to advance gut microbiome research and gut microbiome-based theragnostics.

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Beckers, Bram, Michiel Op De Beeck, Nele Weyens, Rebecca Van Acker, Marc Van Montagu, Wout Boerjan e Jaco Vangronsveld. "Lignin engineering in field-grown poplar trees affects the endosphere bacterial microbiome". Proceedings of the National Academy of Sciences 113, n. 8 (11 gennaio 2016): 2312–17. http://dx.doi.org/10.1073/pnas.1523264113.

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Cinnamoyl-CoA reductase (CCR), an enzyme central to the lignin biosynthetic pathway, represents a promising biotechnological target to reduce lignin levels and to improve the commercial viability of lignocellulosic biomass. However, silencing of the CCR gene results in considerable flux changes of the general and monolignol-specific lignin pathways, ultimately leading to the accumulation of various extractable phenolic compounds in the xylem. Here, we evaluated host genotype-dependent effects of field-grown, CCR-down-regulated poplar trees (Populus tremula × Populus alba) on the bacterial rhizosphere microbiome and the endosphere microbiome, namely the microbiota present in roots, stems, and leaves. Plant-associated bacteria were isolated from all plant compartments by selective isolation and enrichment techniques with specific phenolic carbon sources (such as ferulic acid) that are up-regulated in CCR-deficient poplar trees. The bacterial microbiomes present in the endosphere were highly responsive to the CCR-deficient poplar genotype with remarkably different metabolic capacities and associated community structures compared with the WT trees. In contrast, the rhizosphere microbiome of CCR-deficient and WT poplar trees featured highly overlapping bacterial community structures and metabolic capacities. We demonstrate the host genotype modulation of the plant microbiome by minute genetic variations in the plant genome. Hence, these interactions need to be taken into consideration to understand the full consequences of plant metabolic pathway engineering and its relation with the environment and the intended genetic improvement.

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Maier, Lisa. "Pioneering microbiome engineering". Nature Reviews Microbiology 21, n. 10 (12 settembre 2023): 630. http://dx.doi.org/10.1038/s41579-023-00949-4.

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Han, Kai, Jin Xu, Fang Xie, Julia Crowther e James J. Moon. "Engineering Strategies to Modulate the Gut Microbiome and Immune System". Journal of Immunology 212, n. 2 (15 gennaio 2024): 208–15. http://dx.doi.org/10.4049/jimmunol.2300480.

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Abstract The gut microbiota, predominantly residing in the colon, is a complex ecosystem with a pivotal role in the host immune system. Dysbiosis of the gut microbiota has been associated with various diseases, and there is an urgent need to develop new therapeutics that target the microbiome and restore immune functions. This Brief Review discusses emerging therapeutic strategies that focus on oral delivery systems for modulating the gut microbiome. These strategies include genetic engineering of probiotics, probiotic-biomaterial hybrids, dietary fibers, and oral delivery systems for microbial metabolites, antimicrobial peptides, RNA, and antibiotics. Engineered oral formulations have demonstrated promising outcomes in reshaping the gut microbiome and influencing immune responses in preclinical studies. By leveraging these approaches, the interplay between the gut microbiota and the immune system can be harnessed for the development of novel therapeutics against cancer, autoimmune disorders, and allergies.

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Petrushin, Ivan S., Nadezhda V. Filinova e Daria I. Gutnik. "Potato Microbiome: Relationship with Environmental Factors and Approaches for Microbiome Modulation". International Journal of Molecular Sciences 25, n. 2 (6 gennaio 2024): 750. http://dx.doi.org/10.3390/ijms25020750.

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Every land plant exists in a close relationship with microbial communities of several niches: rhizosphere, endosphere, phyllosphere, etc. The growth and yield of potato—a critical food crop worldwide—highly depend on the diversity and structure of the bacterial and fungal communities with which the potato plant coexists. The potato plant has a specific part, tubers, and the soil near the tubers as a sub-compartment is usually called the “geocaulosphere”, which is associated with the storage process and tare soil microbiome. Specific microbes can help the plant to adapt to particular environmental conditions and resist pathogens. There are a number of approaches to modulate the microbiome that provide organisms with desired features during inoculation. The mechanisms of plant–bacterial communication remain understudied, and for further engineering of microbiomes with particular features, the knowledge on the potato microbiome should be summarized. The most recent approaches to microbiome engineering include the construction of a synthetic microbial community or management of the plant microbiome using genome engineering. In this review, the various factors that determine the microbiome of potato and approaches that allow us to mitigate the negative impact of drought and pathogens are surveyed.

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Lee, Hui, Haosheng Shen, In Hwang, Hua Ling, Wen Yew, Yung Lee e Matthew Chang. "Targeted Approaches for In Situ Gut Microbiome Manipulation". Genes 9, n. 7 (12 luglio 2018): 351. http://dx.doi.org/10.3390/genes9070351.

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Microbial communities and their collective genomes form the gut microbiome, of which bacteria are the major contributor. Through their secreted metabolites, bacteria interact with the host, influencing human health and physiology. Perturbation of the microbiota and metabolome has been associated with various diseases and metabolic conditions. As knowledge on fundamental host-microbiome interactions and genetic engineering tools becomes readily available, targeted manipulation of the gut microbiome for therapeutic applications gains favourable attention. Manipulation of the gut microbiome can be achieved by altering the microbiota population and composition, or by modifying the functional metabolic activity of the microbiome to promote health and restore the microbiome balance. In this article, we review current works that demonstrate various strategies employed to manipulate the gut microbiome in situ to various degrees of precision.

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Naitam, Mayur, e T. V. Abiraami. "MAP’s Assisted Microbiome Engineering". International Journal of Current Microbiology and Applied Sciences 8, n. 05 (10 maggio 2019): 758–63. http://dx.doi.org/10.20546/ijcmas.2019.805.089.

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Cho, Young-Dan, Kyoung-Hwa Kim, Yong-Moo Lee, Young Ku e Yang-Jo Seol. "Oral Microbiome and Host Health: Review on Current Advances in Genome-Wide Analysis". Applied Sciences 11, n. 9 (29 aprile 2021): 4050. http://dx.doi.org/10.3390/app11094050.

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The oral microbiome is an important part of the human microbiome. The oral cavity has the second largest microbiota after the intestines, and its open structure creates a special environment. With the development of technology such as next-generation sequencing and bioinformatics, extensive in-depth microbiome studies have become possible. They can also be applied in the clinical field in terms of diagnosis and treatment. Many microbiome studies have been performed on oral and systemic diseases, showing a close association between the two. Understanding the oral microbiome and host interaction is expected to provide future directions to explore the functional and metabolic changes in diseases, and to uncover the molecular mechanisms for drug development and treatment that facilitate personalized medicine. The aim of this review was to provide comprehension regarding research trends in oral microbiome studies and establish the link between oral microbiomes and systemic diseases based on the latest technique of genome-wide analysis.

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Ameen, Ayesha, Muhammad Nadeem Akram, Sana Farooq, Mehreen Fatima, Hassan Raza, Rabia Naz, Umer Aziz, Mariyam Aziz, Syed Tahir e Athar Hussain. "Gut Microbiome and its Role in the Development of Neurological Disorder (Schizophrenia)". Pakistan Journal of Medical and Health Sciences 17, n. 5 (26 giugno 2023): 311–16. http://dx.doi.org/10.53350/pjmhs2023175311.

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Purpose: The gut microbiome, defined as the community of microorganisms residing in the digestive tract, is believed to play a crucial role in the development of neurological disorders, including schizophrenia. Design: Recent research indicates that individuals with schizophrenia have altered gut microbiomes, characterized by reduced levels of beneficial bacteria such as Bifidobacterium and Lactobacillus, and increased levels of potentially harmful bacteria, such as Proteobacteria. Findings: Furthermore, studies show that the communication between the gut and the brain, known as the gut-brain axis, is disrupted in individuals with schizophrenia. While the exact mechanisms underlying the association between the gut microbiome and schizophrenia are not yet fully understood, researchers suggest that changes in the gut microbiome may affect the immune system and neurotransmitters, which in turn contribute to the development of the disorder Practical Implication: Targeting the gut microbiome through interventions like probiotics and the Mediterranean diet may offer a promising therapeutic approach for individuals with schizophrenia. Conclusion: However, more research is needed to fully comprehend the complex interplay between the gut microbiome and schizophrenia, including the specific mechanisms by which the gut microbiome contributes to the development of the disorder. Keywords: Gut Microbiome. Microbiota, Immune cells, Schizophrenia

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Souza, Priscila Agustinha Neves, Camila Cinto Lima, Nilson Ferrari Junior, Guilherme Guimarães Silva, Ana Laura Abreu Oliveira, Ana Caroline de Melo Gella, Paloma Luiza Rezende Novaes, Vinícius Freire Linares, Leonardo Fonseca Gondim e Amanda Carolina Zicatti da Silveira. "Microbioma intestinal e doença renal crônica: uma relação emergente". Revista Eletrônica Acervo Saúde 23, n. 12 (22 dicembre 2023): e15054. http://dx.doi.org/10.25248/reas.e15054.2023.

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Objetivo: Avaliar a relação entre as alterações no microbioma intestinal e a progressão da doença renal crônica (DRC), bem como as complicações associadas e as potenciais intervenções terapêuticas voltadas ao microbioma intestinal que poderiam ser efetivas. Métodos: Trata-se de uma Revisão Integrativa, realizada por meio da plataforma de base de dados PubMed, com o intento de localizar fontes relevantes para o estudo. A pesquisa foi realizada através da estratégia de pesquisa (("Gastrointestinal Microbiome"[MeSH]) OR (Gut Microbiome)) AND ("Renal Insufficiency, Chronic"[MeSH]), para a busca dos artigos, resultando em 309 artigos iniciais. Dentre esses, devido aos critérios de inclusão e exclusão, 20 tornaram-se fontes oficiais. Resultados: Os estudos apontam que há uma estreita relação entre a microbiota intestinal e a progressão da Doença Renal Crônica, em que a modulação do eixo intestino-rim é um potencial alvo terapêutico. Considerações finais: A relação entre a microbiota intestinal e a DRC é evidente, porém, mais pesquisas na área são necessárias para esclarecimento e confirmação das hipóteses.

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Wang, Nicole R., e Cara H. Haney. "Harnessing the genetic potential of the plant microbiome". Biochemist 42, n. 4 (29 luglio 2020): 20–25. http://dx.doi.org/10.1042/bio20200042.

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Plant-associated microorganisms, such as bacteria and fungi, can grow on and survive in healthy plant tissues, making up the plant microbiome. Members of the plant microbiome can provide benefits to their host, and emerging research suggests that plants can reshape the composition of their microbiomes in response to environmental cues. The plant microbiome collectively acts as a reservoir for genes that may improve plant growth and survival in response to challenges, therefore contributing to the total genetic potential of the plant. Understanding the impact of the plant microbiome has unlocked new strategies for improving crop production, especially as climate change threatens to increase the prevalence of pathogens and stressful growth conditions. Applying microbiome engineering strategies, such as inoculation with plant growth-promoting rhizobacteria (PGPR), and incorporating the microbiome into the breeding process show promise for improving future agricultural crop production.

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Afridi, Muhammad Siddique, Sher Ali, Abdul Salam, Willian César Terra, Aqsa Hafeez, Sumaira, Baber Ali et al. "Plant Microbiome Engineering: Hopes or Hypes". Biology 11, n. 12 (7 dicembre 2022): 1782. http://dx.doi.org/10.3390/biology11121782.

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Rhizosphere microbiome is a dynamic and complex zone of microbial communities. This complex plant-associated microbial community, usually regarded as the plant’s second genome, plays a crucial role in plant health. It is unquestioned that plant microbiome collectively contributes to plant growth and fitness. It also provides a safeguard from plant pathogens, and induces tolerance in the host against abiotic stressors. The revolution in omics, gene-editing and sequencing tools have somehow led to unravel the compositions and latent interactions between plants and microbes. Similarly, besides standard practices, many biotechnological, (bio)chemical and ecological methods have also been proposed. Such platforms have been solely dedicated to engineer the complex microbiome by untangling the potential barriers, and to achieve better agriculture output. Yet, several limitations, for example, the biological obstacles, abiotic constraints and molecular tools that capably impact plant microbiome engineering and functionality, remained unaddressed problems. In this review, we provide a holistic overview of plant microbiome composition, complexities, and major challenges in plant microbiome engineering. Then, we unearthed all inevitable abiotic factors that serve as bottlenecks by discouraging plant microbiome engineering and functionality. Lastly, by exploring the inherent role of micro/macrofauna, we propose economic and eco-friendly strategies that could be harnessed sustainably and biotechnologically for resilient plant microbiome engineering.

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Rehman, Khurram. "Postnatal Variation in Microbiota Compositional Dynamics of Infants of Cesarean versus Vaginal mode of Delivery". Clinical Research Notes 2, n. 2 (15 novembre 2021): 01–10. http://dx.doi.org/10.31579/2690-8816/041.

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Introduction: Human microbial communities’ influences human physiology but, how they attain unique taxonomical and functional signatures within each body is still underexplored. Many studies have characterized that shape and composition of infant’s microbiome is substantially dependent upon the delivery mode at birth. The epidemiological data have shown C-section delivered babies are failed to exposed to maternal vaginal microbiota so they develop altered bacterial communities or microbiome that increases the risk of metabolic disorders later in life. The microbiota composition of C-section delivered babies is quick different from the infants deliver vaginally which expose to vaginal fluid during birth. C-section delivered babies acquire different microbiota from vaginally delivered infants as they exposing to vaginal fluid during birth. Following this, various postnatal factors are involving in the modulation of infant's microbiome composition such as exposure of different environmental conditions, antibiotic intake, diet, genetics and body sites that negatively influences the infant’s immune system. Objectives: In this review, it is intended to describe the variation in shape and composition of microbiome of vaginally and cesarean delivered babies and how microbiome's composition and immune system development is affected by various postnatal factors. In this study, homeostatic aspects of Cesarean delivered babies are also being discussed as it is also affected by the postnatal microbiome-mediated pathogen, variation in gut, oral and body sites bacterial communities. Conclusion: We concluded that cesarean delivered children showed significantly immune deficiencies which make them more prone to various disorders such as arthritis, asthma, allergic diseases, connective tissues diseases, leukemia and inflammatory bowel syndrome. These finding are highlighting the importance of shape and composition of microbiome in early-life.

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Marsh, James W., e Ruth E. Ley. "Microbiome engineering: Taming the untractable". Cell 185, n. 3 (febbraio 2022): 416–18. http://dx.doi.org/10.1016/j.cell.2021.12.034.

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Verstraete, Willy. "The microbiome as engineering tool". New Biotechnology 33 (luglio 2016): S54. http://dx.doi.org/10.1016/j.nbt.2016.06.913.

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Donia, Mohamed S. "A Toolbox for Microbiome Engineering". Cell Systems 1, n. 1 (luglio 2015): 21–23. http://dx.doi.org/10.1016/j.cels.2015.07.003.

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Inda, María Eugenia, Esther Broset, Timothy K. Lu e Cesar de la Fuente-Nunez. "Emerging Frontiers in Microbiome Engineering". Trends in Immunology 40, n. 10 (ottobre 2019): 952–73. http://dx.doi.org/10.1016/j.it.2019.08.007.

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Singh, Vineet, Youn-Chul Ryu e Tatsuya Unno. "Dietary Intervention Induced Distinct Repercussions in Response to the Individual Gut Microbiota as Demonstrated by the In Vitro Fecal Fermentation of Beef". Applied Sciences 11, n. 15 (25 luglio 2021): 6841. http://dx.doi.org/10.3390/app11156841.

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Animals and humans have very different gut microbiota, and the human microbiota is unique to each individual. For these reasons, it is difficult to find a diet that provides all the nutrients according to individual requirements. In this study, we investigated the possibility of using simple in vitro fecal fermentation of digested food to evaluate fundamental differences in the gut metabolism of individuals with different microbiomes in response to specific dietary interventions. We fermented beef using six human fecal microbiotas, analyzed shifts in these microbiomes, and quantified short-chain fatty acid (SCFA) production in each system. Our results demonstrate that each microbiome responds with a unique shift in composition, SCFA production, and metabolic activity following 90 min of fecal fermentation of beef. Differentially abundant genera and metabolic activities varied among subjects. Only two subjects’ fecal microbiome showed no significant changes in their metabolic activity, while the other subjects’ microbial metagenome showed anywhere between 17 and 60 differences in their metabolism, including several changes associated with heart disease (i.e., depletion of oleate and palmitoleate biosynthesis). This study revealed the varying responses of each microbiome when exposed to digested beef, suggesting that this method could provide fundamental information in understanding personal nutrient requirements and the impact of changes in the individual gut microbiota on human health. Although further studies using larger study populations are required, this study describes a simple and cost-effective protocol for evaluating the interactions between specific dietary interventions and individual gut microbiota differences.

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Quides, Kenjiro W., e Hagop S. Atamian. "A microbiome engineering framework to evaluate rhizobial symbionts of legumes". Plant and Soil 463, n. 1-2 (4 marzo 2021): 631–42. http://dx.doi.org/10.1007/s11104-021-04892-2.

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Abstract Background For well over a century, rhizobia have been recognized as effective biofertilizer options for legume crops. This has led to the widespread use of rhizobial inoculants in agricultural systems, but a recurring issue has emerged: applied rhizobia struggle to provide growth benefits to legume crops. This has largely been attributed to the presence of soil rhizobia and has been termed the ‘rhizobial competition problem.’ Scope Microbiome engineering has emerged as a methodology to circumvent the rhizobial competition problem by creating legume microbiomes that do not require exogenous rhizobia. However, we highlight an alternative implementation of microbiome engineering that focuses on untangling the complexities of the symbiosis that contribute to the rhizobial competition problem. We outline three approaches that use different starting inocula to test hypotheses to overcome the rhizobial competition problem. Conclusions The approaches we suggest are targeted at various stages of the legume-rhizobium symbiosis and will help us uncover underlying molecular mechanisms that contribute to the rhizobial competition problem. We conclude with an integrative perspective of these different approaches and suggest a path forward for future research on legumes and their complex microbiome.

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Chitayat Levi, Liyam, Ido Rippin, Moran Ben Tulila, Rotem Galron e Tamir Tuller. "Modulating Gene Expression within a Microbiome Based on Computational Mmodels". Biology 11, n. 9 (31 agosto 2022): 1301. http://dx.doi.org/10.3390/biology11091301.

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Recent research in the field of bioinformatics and molecular biology has revealed the immense complexity and uniqueness of microbiomes, while also showcasing the impact of the symbiosis between a microbiome and its host or environment. A core property influencing this process is horizontal gene transfer between members of the bacterial community used to maintain genetic variation. The essential effect of this mechanism is the exposure of genetic information to a wide array of members of the community, creating an additional “layer” of information in the microbiome named the “plasmidome”. From an engineering perspective, introduction of genetic information to an environment must be facilitated into chosen species which will be able to carry out the desired effect instead of competing and inhibiting it. Moreover, this process of information transfer imposes concerns for the biosafety of genetic engineering of microbiomes as exposure of genetic information into unwanted hosts can have unprecedented ecological impacts. Current technologies are usually experimentally developed for a specific host/environment, and only deal with the transformation process itself at best, ignoring the impact of horizontal gene transfer and gene-microbiome interactions that occur over larger periods of time in uncontrolled environments. The goal of this research was to design new microbiome-specific versions of engineered genetic information, providing an additional layer of compatibility to existing engineering techniques. The engineering framework is entirely computational and is agnostic to the selected microbiome or gene by reducing the problem into the following set up: microbiome species can be defined as wanted or unwanted hosts of the modification. Then, every element related to gene expression (e.g., promoters, coding regions, etc.) and regulation is individually examined and engineered by novel algorithms to provide the defined expression preferences. Additionally, the synergistic effect of the combination of engineered gene blocks facilitates robustness to random mutations that might occur over time. This method has been validated using both computational and experimental tools, stemming from the research done in the iGEM 2021 competition, by the TAU group.

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Ferraz, Maria Pia. "An Overview of the Relevance of Human Gut and Skin Microbiome in Disease: The Influence on Atopic Dermatitis". Applied Sciences 13, n. 18 (21 settembre 2023): 10540. http://dx.doi.org/10.3390/app131810540.

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It is acknowledged that humans have a diverse and abundant microbial community known as the human microbiome. Nevertheless, our comprehension of the numerous functions these microorganisms have in human health is still in its early stages. Microorganisms belonging to the human microbiome typically coexist with their host, but in certain situations, they can lead to diseases. They are found in several areas of the human body in healthy individuals. The microbiome is highly diverse, and its composition varies depending on the body site. It primarily comprises bacteria that are crucial for upholding a state of well-being and equilibrium. The microbiome’s influence on atopic dermatitis development was, therefore, analyzed. The importance of maintaining a balanced and functional commensal microbiota, as well as the use of prebiotics and probiotics in the prevention and treatment of atopic dermatitis were also explored. The skin microbiome’s association with atopic dermatitis will allow for a better understanding of pathogenesis and also exploring new therapeutic approaches, making the skin microbiome an increasingly relevant therapeutic target.

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ółkiewicz, Jakub Z˙, Aleksandra Marzec e Wong Jest Phia. "Postbiotics—A Revolution Engineering Symbiotics ofInanimate microorganisms and their components". International Journal of Scientific Research and Management (IJSRM) 12, n. 05 (26 maggio 2024): 1039–55. http://dx.doi.org/10.18535/ijsrm/v12i05.mp03.

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As an imbalance in the intestinal microbiota can lead to the development of several diseases (e.g., type 1 diabetes, cancer, among others), the use of prebiotics, probiotics, and postbiotics to alter the gut microbiome has attracted recent interest. Postbiotics include any substance released by or produced through the metabolic activity of the microorganism, which exerts a beneficial effect on the host, directly or indirectly. As postbiotics do not contain live microorganisms, the risks associated with their intake are minimized. Here, we provided a critical review of postbiotics described in the literature, including their mechanisms of action, clinical characteristics, and potential therapeutic applications. We detailed the pleiotropic effects of postbiotics, including their immunomodulatory, anti-inflammatory, antioxidant, and anti-cancer properties. Although the use of postbiotics is an attractive strategy for altering the microbiome, further study into its efficacy and safety is warranted.

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Yim, Sung Sun, e Harris H. Wang. "Exploiting interbacterial antagonism for microbiome engineering". Current Opinion in Biomedical Engineering 19 (settembre 2021): 100307. http://dx.doi.org/10.1016/j.cobme.2021.100307.

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García-Jiménez, Beatriz, Tomás de la Rosa e Mark D. Wilkinson. "MDPbiome: microbiome engineering through prescriptive perturbations". Bioinformatics 34, n. 17 (1 settembre 2018): i838—i847. http://dx.doi.org/10.1093/bioinformatics/bty562.

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Yadav, Brijesh, Sukanta S. Bhattacharya, Lauren Rosen, Ravinder Nagpal, Hariom Yadav e Jagjit S. Yadav. "Oro-Respiratory Dysbiosis and Its Modulatory Effect on Lung Mucosal Toxicity during Exposure or Co-Exposure to Carbon Nanotubes and Cigarette Smoke". Nanomaterials 14, n. 3 (4 febbraio 2024): 314. http://dx.doi.org/10.3390/nano14030314.

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The oro-respiratory microbiome is impacted by inhalable exposures such as smoking and has been associated with respiratory health conditions. However, the effect of emerging toxicants, particularly engineered nanoparticles, alone or in co-exposure with smoking, is poorly understood. Here, we investigated the impact of sub-chronic exposure to carbon nanotube (CNT) particles, cigarette smoke extract (CSE), and their combination. The oral, nasal, and lung microbiomes were characterized using 16S rRNA-based metagenomics. The exposures caused the following shifts in lung microbiota: CNT led to a change from Proteobacteria and Bacteroidetes to Firmicutes and Tenericutes; CSE caused a shift from Proteobacteria to Bacteroidetes; and co-exposure (CNT+CSE) had a mixed effect, maintaining higher numbers of Bacteroidetes (due to the CNT effect) and Tenericutes (due to the CSE effect) compared to the control group. Oral microbiome analysis revealed an abundance of the following genera: Acinetobacter (CNT), Staphylococcus, Aggregatibacter, Allobaculum, and Streptococcus (CSE), and Alkalibacterium (CNT+CSE). These proinflammatory microbial shifts correlated with changes in the relative expression of lung mucosal homeostasis/defense proteins, viz., aquaporin 1 (AQP-1), surfactant protein A (SP-A), mucin 5b (MUC5B), and IgA. Microbiota depletion reversed these perturbations, albeit to a varying extent, confirming the modulatory role of oro-respiratory dysbiosis in lung mucosal toxicity. This is the first demonstration of specific oro-respiratory microbiome constituents as potential modifiers of toxicant effects in exposed lungs.

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Nadarajah, Kalaivani, e Nur Sabrina Natasha Abdul Rahman. "The Microbial Connection to Sustainable Agriculture". Plants 12, n. 12 (14 giugno 2023): 2307. http://dx.doi.org/10.3390/plants12122307.

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Microorganisms are an important element in modeling sustainable agriculture. Their role in soil fertility and health is crucial in maintaining plants’ growth, development, and yield. Further, microorganisms impact agriculture negatively through disease and emerging diseases. Deciphering the extensive functionality and structural diversity within the plant–soil microbiome is necessary to effectively deploy these organisms in sustainable agriculture. Although both the plant and soil microbiome have been studied over the decades, the efficiency of translating the laboratory and greenhouse findings to the field is largely dependent on the ability of the inoculants or beneficial microorganisms to colonize the soil and maintain stability in the ecosystem. Further, the plant and its environment are two variables that influence the plant and soil microbiome’s diversity and structure. Thus, in recent years, researchers have looked into microbiome engineering that would enable them to modify the microbial communities in order to increase the efficiency and effectiveness of the inoculants. The engineering of environments is believed to support resistance to biotic and abiotic stressors, plant fitness, and productivity. Population characterization is crucial in microbiome manipulation, as well as in the identification of potential biofertilizers and biocontrol agents. Next-generation sequencing approaches that identify both culturable and non-culturable microbes associated with the soil and plant microbiome have expanded our knowledge in this area. Additionally, genome editing and multidisciplinary omics methods have provided scientists with a framework to engineer dependable and sustainable microbial communities that support high yield, disease resistance, nutrient cycling, and management of stressors. In this review, we present an overview of the role of beneficial microbes in sustainable agriculture, microbiome engineering, translation of this technology to the field, and the main approaches used by laboratories worldwide to study the plant–soil microbiome. These initiatives are important to the advancement of green technologies in agriculture.

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Theriot, Casey M. "Beyond Structure: Defining the Function of the Gut Using Omic Approaches for Rational Design of Personalized Therapeutics". mSystems 3, n. 2 (6 marzo 2018): e00173-17. http://dx.doi.org/10.1128/msystems.00173-17.

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ABSTRACT Over the past 10 years, microbiome research has focused on defining the structures associated with different disease states in multiple systems, but has fallen short on showing causation. Prior omic studies have generated many new hypotheses, but moving forward we need to start dissecting the function of each bacterium alone and in concert with complex bacterial communities in well-characterized systems. Over the next 5 years, we need a merging of new omic technologies for exploratory studies with classical bacterial genetics, bacterial physiology, protein engineering, and biochemistry to further define the biochemical mechanisms of the gut microbiota. The future of the systems microbiology field will focus on targeted engineering and editing of the microbiome to alter function, which will be leveraged to prevent and/or treat human diseases. This perspective will focus on my contribution to the microbiome field, both past and present, and where I think research in the field is headed in the near future.

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Fang, Jingyun, Jiayu Yin, Qinghong Liu, Xiangyi Yang, Xuesong He, Shengzhou Wang, Min Fan et al. "Improvement of Clinical Symptoms and Gut Microbiome After Fecal Microbiota Transplantation: A Case Study of a 106-Year-Old Man with MODS". Proceedings of Anticancer Research 6, n. 1 (19 gennaio 2022): 1–5. http://dx.doi.org/10.26689/par.v6i1.2840.

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Fecal microbiota transplantation (FMT) has been used in a wide variety of diseases. Many researchers hypothesize that the dysbiosis of intestinal microbiota plays an important role in the development of gut-derived infections; thus, FMT is a potential therapeutic target against multiple organ dysfunction syndrome (MODS). A 106-year-old male patient was initially diagnosed with cerebral infarction and pulmonary infection. During the course of hospitalization, the patient developed MODS. The patient received a single nasogastric infusion of sterile-filtered, pathogen-free feces from a healthy donor. Fecal samples were collected every two days post-infusion to monitor changes in the microbiota composition in response to treatment. After FMT, MODS and severe diarrhea were alleviated; the patient’s fecal microbiome diversity resembled that of the healthy donor’s fecal microbiome; moreover, his clinical symptoms improved remarkably with the changes in fecal microbiome. Additionally, no observable side effects were noted during FMT treatment. These findings warrant further investigation of FMT as a putative new therapy for treating microbiota-related diseases, such as MODS.

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Dries, Leonie, Maximilian Hendgen, Sylvia Schnell, Otmar Löhnertz e Anne Vortkamp. "Rhizosphere engineering: leading towards a sustainable viticulture?" OENO One 55, n. 2 (11 giugno 2021): 353–63. http://dx.doi.org/10.20870/oeno-one.2021.55.2.4534.

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Microorganisms are a substantial component of the rhizosphere, and the activity and composition of rhizosphere microbial populations markedly affect interactions between plants and the soil environment. In addition, the microbiota of the rhizosphere can positively influence plant development, growth and vitality. In vineyards, management practices influence both grapevine root growth directly and the rhizosphere microbiota, but the exact mode of action is largely unknown. Recently, however, two new research approaches are increasingly coming into focus to enhance grapevine growth and health: plant engineering and rhizosphere engineering. In plant engineering, knowledge about plant-microbiome interactions is used for plant breeding strategies. In rhizosphere engineering, microbial communities are modified by adding specific fertilisers, nutrients or by bio-inoculation with certain bacteria and/or fungi. Taken together, these new methods suggest a potential for reaching a more sustainable development of pesticide-reduced viticulture in the future.

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Vieira-Baptista, Pedro, Francesco De Seta, Hans Verstraelen, Gary Ventolini, Risa Lonnee-Hoffmann e Ahinoam Lev-Sagie. "The Vaginal Microbiome: V. Therapeutic Modalities of Vaginal Microbiome Engineering and Research Challenges". Journal of Lower Genital Tract Disease 26, n. 1 (gennaio 2022): 99–104. http://dx.doi.org/10.1097/lgt.0000000000000647.

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Whitfill, Travis, e Julia Oh. "Recoding the metagenome: microbiome engineering in situ". Current Opinion in Microbiology 50 (agosto 2019): 28–34. http://dx.doi.org/10.1016/j.mib.2019.09.005.

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Kessell, Aimee K., Hugh C. McCullough, Jennifer M. Auchtung, Hans C. Bernstein e Hyun-Seob Song. "Predictive interactome modeling for precision microbiome engineering". Current Opinion in Chemical Engineering 30 (dicembre 2020): 77–85. http://dx.doi.org/10.1016/j.coche.2020.08.003.

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Foo, Jee Loon, Hua Ling, Yung Seng Lee e Matthew Wook Chang. "Microbiome engineering: Current applications and its future". Biotechnology Journal 12, n. 3 (30 gennaio 2017): 1600099. http://dx.doi.org/10.1002/biot.201600099.

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Epstein, Hannah E., Hillary A. Smith, Gergely Torda e Madeleine JH Oppen. "Microbiome engineering: enhancing climate resilience in corals". Frontiers in Ecology and the Environment 17, n. 2 (4 febbraio 2019): 100–108. http://dx.doi.org/10.1002/fee.2001.

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March, John C., e Matthew Wook Chang. "Microbiome Engineering: A New Generation of Ideas". Biotechnology Journal 15, n. 10 (ottobre 2020): 2000406. http://dx.doi.org/10.1002/biot.202000406.

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Tkach, S. M., A. E. Dorofeyev e L. M. Ryzhii. "Current insights into microbiome-based therapy. Review". Modern Gastroenterology, n. 1 (29 febbraio 2024): 73–80. http://dx.doi.org/10.30978/mg-2024-1-73.

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Over the past decades, it has become apparent that a human body is inextricably intertwined with the microbiome. The latter exchanges metabolites with a host’s organism, protects it from infectious agents and is necessary for the normal immune system development. Microbiome can also respond to any changes in a host body and becomes altered («dysbiotic») during diseases or pathological conditions. The exchange between the host and the microbiome occurs constantly, it is bidirectional and integral both during a healthy state and during disease. Therefore, there is considerable interest in microbiome‑based therapy (BM) for a wide range of human diseases. The microbiome is a multi‑level ecological system, and any approach that alters any component of that system can be considered as MBT, or in other words, microbiota therapy. Recently, significant progress has been made in the development of live biologics that help to restore normal gut microbiota and treat various diseases, including Clostridium difficile infection (CDI). Currently, the most common types of MBT are: 1) fecal microbiota transplantation (FMT); 2) a certain consortium of known microbes delivered orally or instilled into the gastrointestinal tract; 3) addition of microbial metabolites (for example, short‑chain fatty acids, butyrate). Interest in the intestinal microbiota has especially increased after the establishment of excellent therapeutic efficacy of FMT at CDI, as well as other intestinal diseases and some extraintestinal diseases that are difficult to treat with traditional methods. This promoted the study of the effectiveness and safety of MBT, such as classical and defined (selective) TFM, treatment with faecal spores or non‑toxigenic strains of C. difficile, classical or new commensal probiotics, bacteriophages or recombinant live biotherapeutic products. This completely new line of treatment, despite its short history, has ushered in a new era in the improvement of treatment aimed at intestinal and metabolic disorders.

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Djuryak, V. S., A. O. Mikheev, L. I. Sydorchuk e I. V. Pankiv. "The state of the colon microbiome in women with gestational diabetes". INTERNATIONAL JOURNAL OF ENDOCRINOLOGY (Ukraine) 19, n. 4 (18 luglio 2023): 284–89. http://dx.doi.org/10.22141/2224-0721.19.4.2023.1287.

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Background. Gestational diabetes is a condition that arises due to impaired metabolic processes against the background of insulin resistance and an increase in blood glucose levels during pregnancy. This pathology leads to a significant number of pregnancy and childbirth complications, high child perinatal morbidity and mortality, and its prevalence varies throughout the world. The aim of the work was to determine the taxonomic composition, population level and microecological indicators of the macroorganism-microbiome ecosystem of the symbiotic colon microbiota in women with gestational diabetes. Materials and methods. The microbiological examination of the colon contents was carried out in 26 pregnant women aged 18 to 35 years. The clinical material for microbiological examination was the fresh colon contents (faeces) taken from medium portions, which were collected in sterile (after autoclaving) vials. Results. According to the results of the work, it was found that during gestational diabetes, the taxonomic composition and microecological parameters of the macroorganism-microbiome ecosystem of the colon microbiota in women are impaired due to the biotope contamination with pathogenic microorganisms (E.coli HLy+) and opportunistic pathogens (E.coli Lac-, P.mirabilis, P.vulgaris, E.cloacae, C.diversus, S.marcescens), enterobacteria, C.albicans, P.niger and bacteria of the genus Clostridium. Alterations in the taxonomic composition and microecological indicators of the colon microbiome in women with gestational diabetes lead to multidirectional changes depending on the taxon: a decrease in the population level of bacteria, which are the most important in terms of representation in the human colon microbiome, with a multifunctional role in maintaining microecological homeostasis (bacteria of the genus Bifidobacterium — by 17.59 %, Lactobacillus — by 38.37 %) and an increase or a stable trend towards an increase in the population level of opportunistic enterobacteria P.mirabilis by 26.67 %; among other enterobacteria, the population reaches high levels (from 6.390 ± 0.009 lg CFU/g to 7.46 ± 0.17 lg CFU/g), the level of Staphylococcus in increased by 35.94 %, C.albicans — by 26.74 %, P.melaninogenicus — by 55.93 %.

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Tabbabi, Ahmed, Daiki Mizushima, Daisuke S. Yamamoto e Hirotomo Kato. "Sand Flies and Their Microbiota". Parasitologia 2, n. 2 (11 aprile 2022): 71–87. http://dx.doi.org/10.3390/parasitologia2020008.

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Sand flies are a significant public health concern in many parts of the world where they are known to transmit agents of several zoonotic diseases to humans, such as leishmaniasis. Vector control remains a key component of many anti-leishmaniasis programs and probably will remain so until an effective vaccine becomes available. The sand fly gut microbiota has recently emerged as an encouraging field for the exploration of vector-based disease control. In particular, the gut microbiome was previously reported to either enhance or inhibit parasite activity depending on the species of bacteria and, thus, has the potential to alter vector competence. Here, we describe the technological advances that are currently expanding our understanding of microbiota composition in sand flies. The acquisition and composition of microbiomes are influenced by several abiotic and biotic factors, including host immunity, genetics, and the environment. Therefore, the microbiomes of sand flies can vary substantially between individuals, life stages, species, and over geographical space, and this variation likely contributes to differences in host phenotypes, highlighting opportunities for novel vector control strategies.

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Petrushin, Ivan S., Ilia A. Vasilev e Yulia A. Markova. "Drought Tolerance of Legumes: Physiology and the Role of the Microbiome". Current Issues in Molecular Biology 45, n. 8 (28 luglio 2023): 6311–24. http://dx.doi.org/10.3390/cimb45080398.

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Water scarcity and global warming make drought-tolerant plant species more in-demand than ever. The most drastic damage exerted by drought occurs during the critical growth stages of seed development and reproduction. In the course of their evolution, plants form a variety of drought-tolerance mechanisms, including recruiting beneficial microorganisms. Legumes (one of the three largest groups of higher plants) have unique features and the potential to adapt to abiotic stress. The available literature discusses the genetic (breeding) and physiological aspects of drought tolerance in legumes, neglecting the role of the microbiome. Our review aims to fill this gap: starting with the physiological mechanisms of legume drought adaptation, we describe the symbiotic relationship of the plant host with the microbial community and its role in facing drought. We consider two types of studies related to microbiomes in low-water conditions: comparisons and microbiome engineering (modulation). The first type of research includes diversity shifts and the isolation of microorganisms from the various plant niches to which they belong. The second type focuses on manipulating the plant holobiont through microbiome engineering—a promising biotech strategy to improve the yield and stress-resistance of legumes.

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Mendz, George L. "The Vaginal Microbiome during Pregnancy in Health and Disease". Applied Microbiology 3, n. 4 (30 novembre 2023): 1302–38. http://dx.doi.org/10.3390/applmicrobiol3040089.

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This study appraises the progress in the understanding of the composition of the vaginal microflora with a focus on the microbiome during pregnancy. This knowledge is presented with the background of the global health contribution, along with the importance of these microbial communities to pregnancy. A brief review of current methods employed to investigate the structure of these microbial populations is included. Two types of studies, cross-sectional and longitudinal, have been used to characterise the vaginal microbiota; both types are reviewed since they provide information that serves to piece together a more complete picture of the vaginal microflora and its changes during pregnancy. The identity of microbes present in the vagina are examined in the context of health and disease, and, more specifically, in the setting of pregnancy outcomes. The protective role of lactobacilli in maintaining a healthy vaginal environment is evaluated, with analyses of the different roles of various Lactobacillus spp. Classifications of the vaginal microbiota into vagitypes in non-pregnant and pregnant women are discussed. The associations of specific taxa with three adverse pregnancy results, namely, miscarriage, stillbirth, and preterm birth, are examined in some detail. Longitudinal studies investigating changes in the bacterial community composition and taxa abundance demonstrate that this microbiota decreases in richness and diversity relative to those present in non-pregnant microbiomes. Notwithstanding the significant effort made to characterise the vagina bacterial microbiota, a large number of issues remain to be fully understood.

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Burz, Sebastian Dan, Senka Causevic, Alma Dal Co, Marija Dmitrijeva, Philipp Engel, Daniel Garrido-Sanz, Gilbert Greub et al. "From microbiome composition to functional engineering, one step at a time". Microbiology and Molecular Biology Reviews, 10 novembre 2023. http://dx.doi.org/10.1128/mmbr.00063-23.

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SUMMARY Communities of microorganisms (microbiota) are present in all habitats on Earth and are relevant for agriculture, health, and climate. Deciphering the mechanisms that determine microbiota dynamics and functioning within the context of their respective environments or hosts (the microbiomes) is crucially important. However, the sheer taxonomic, metabolic, functional, and spatial complexity of most microbiomes poses substantial challenges to advancing our knowledge of these mechanisms. While nucleic acid sequencing technologies can chart microbiota composition with high precision, we mostly lack information about the functional roles and interactions of each strain present in a given microbiome. This limits our ability to predict microbiome function in natural habitats and, in the case of dysfunction or dysbiosis, to redirect microbiomes onto stable paths. Here, we will discuss a systematic approach (dubbed the N + 1/N−1 concept) to enable step-by-step dissection of microbiome assembly and functioning, as well as intervention procedures to introduce or eliminate one particular microbial strain at a time. The N+1/N−1 concept is informed by natural invasion events and selects culturable, genetically accessible microbes with well-annotated genomes to chart their proliferation or decline within defined synthetic and/or complex natural microbiota. This approach enables harnessing classical microbiological and diversity approaches, as well as omics tools and mathematical modeling to decipher the mechanisms underlying N+1/N−1 microbiota outcomes. Application of this concept further provides stepping stones and benchmarks for microbiome structure and function analyses and more complex microbiome intervention strategies.

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Lawson, Christopher E. "Retooling Microbiome Engineering for a Sustainable Future". mSystems 6, n. 4 (31 agosto 2021). http://dx.doi.org/10.1128/msystems.00925-21.

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Microbial communities (microbiomes) have been harnessed in biotechnology applications such as wastewater treatment and bioremediation for over a century. Traditionally, engineering approaches have focused on shaping the environment to steer microbiome function versus direct manipulation of the microbiome’s metabolic network.

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Brennan, Caitriona, Kristina Chan, Tanya Kumar, Erica Maissy, Linda Brubaker, Marisol I. Dothard, Jack A. Gilbert et al. "Harnessing the Power Within: Engineering the Microbiome for Enhanced Gynecologic Health". Reproduction and Fertility, marzo 2024. http://dx.doi.org/10.1530/raf-23-0060.

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Although numerous studies have demonstrated the impact of microbiome manipulation on human health, research on the microbiome’s influence on female health remains relatively limited despite substantial disease burden. In light of this, we present a selected review of clinical trials and preclinical studies targeting both the vaginal and gut microbiome for the prevention or treatment of various gynecologic conditions. Specifically, we explore studies that leverage microbiota transplants, probiotics, prebiotics, diet modifications, and engineered microbial strains. A healthy vaginal microbiome for females of reproductive age consists of lactic acid-producing bacteria predominantly of the Lactobacillus genus, which serves as a protective barrier against pathogens and maintains a balanced ecosystem. The gut microbiota's production of short-chain fatty acids, metabolism of primary bile acids, and modulation of sex steroid levels have significant implications for the interplay between host and microbes throughout the body, ultimately impacting reproductive health. By harnessing interventions that modulate both the vaginal and gut microbiomes, it becomes possible to not only maintain homeostasis but also mitigate pathological conditions. While the field is still working towards making broad clinical recommendations, the current studies demonstrate that manipulating the microbiome holds great potential for addressing diverse gynecologic conditions.

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Mousavinasab, Fatemehsadat, Ronika karimi, Sima Taheri, Fatemeh Ahmadvand, Saameh Sanaaee, Sajad Najafi, Masood Soltani Halvaii et al. "Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering". Cancer Cell International 23, n. 1 (11 novembre 2023). http://dx.doi.org/10.1186/s12935-023-03095-2.

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AbstractRecent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.

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Tanaka, Tomoki, Ryoga Sugiyama, Yu Sato, Manami Kawaguchi, Kohsuke Honda, Hiroaki Iwaki e Kenji Okano. "Precise microbiome engineering using natural and synthetic bacteriophages targeting an artificial bacterial consortium". Frontiers in Microbiology 15 (2 maggio 2024). http://dx.doi.org/10.3389/fmicb.2024.1403903.

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In natural microbiomes, microorganisms interact with each other and exhibit diverse functions. Microbiome engineering, which enables bacterial knockdown, is a promising method to elucidate the functions of targeted bacteria in microbiomes. However, few methods to selectively kill target microorganisms in the microbiome without affecting the growth of nontarget microorganisms are available. In this study, we focused on the host-specific lytic ability of virulent phages and validated their potency for precise microbiome engineering. In an artificial microbiome consisting of Escherichia coli, Pseudomonas putida, Bacillus subtilis, and Lactiplantibacillus plantarum, the addition of bacteriophages infecting their respective host strains specifically reduced the number of these bacteria more than 102 orders. Remarkably, the reduction in target bacteria did not affect the growth of nontarget bacteria, indicating that bacteriophages were effective tools for precise microbiome engineering. Moreover, a virulent derivative of the λ phage was synthesized from prophage DNA in the genome of λ lysogen by in vivo DNA assembly and phage-rebooting techniques, and E. coli-targeted microbiome engineering was achieved. These results propose a novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains without isolating phages from environmental samples.

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