Jacqueline Boyajian, Paromita Islam, Ahmed Abosalha, Sabrina Schaly, Rahul Thareja, Amal Kassab, Karan Arora, Madison Santos, Cedrique Shum-Tim, Satya Prakash
The global prevalence of obesity currently exceeds 1 billion people and is accompanied by an increase in the aging population. Obesity and aging share many hallmarks and are leading risk factors for cardiometabolic disease and premature death. Current anti-obesity and pro-longevity pharmacotherapies are limited by side effects, warranting the development of novel therapies. The gut microbiota plays a major role in human health and disease, with a dysbiotic composition evident in obese and aged individuals. The bidirectional communication system between the gut and the central nervous system, known as the gut-brain axis, may link obesity to unhealthy aging. Modulating the gut with microbiome-targeted therapies, such as biotics, is a novel strategy to treat and/or manage obesity and promote longevity. Biotics represent material derived from living or once-living organisms, many of which have therapeutic effects. Pre-, pro-, syn- and post-biotics may beneficially modulate gut microbial composition and function to improve obesity and the aging process. However, the investigation of biotics as next-generation therapeutics has only just begun. Further research is needed to identify therapeutic biotics and understand their mechanisms of action. Investigating the function of the gut-brain axis in obesity and aging may lead to novel therapeutic strategies for obese, aged and comorbid (e.g., sarcopenic obese) patient populations. This review discusses the interrelationship between obesity and aging, with a particular emphasis on the gut microbiome, and presents biotics as novel therapeutic agents for obesity, aging and related disease states.
{"title":"Probiotics, prebiotics, synbiotics and other microbiome-based innovative therapeutics to mitigate obesity and enhance longevity via the gut-brain axis","authors":"Jacqueline Boyajian, Paromita Islam, Ahmed Abosalha, Sabrina Schaly, Rahul Thareja, Amal Kassab, Karan Arora, Madison Santos, Cedrique Shum-Tim, Satya Prakash","doi":"10.20517/mrr.2024.05","DOIUrl":"https://doi.org/10.20517/mrr.2024.05","url":null,"abstract":"The global prevalence of obesity currently exceeds 1 billion people and is accompanied by an increase in the aging population. Obesity and aging share many hallmarks and are leading risk factors for cardiometabolic disease and premature death. Current anti-obesity and pro-longevity pharmacotherapies are limited by side effects, warranting the development of novel therapies. The gut microbiota plays a major role in human health and disease, with a dysbiotic composition evident in obese and aged individuals. The bidirectional communication system between the gut and the central nervous system, known as the gut-brain axis, may link obesity to unhealthy aging. Modulating the gut with microbiome-targeted therapies, such as biotics, is a novel strategy to treat and/or manage obesity and promote longevity. Biotics represent material derived from living or once-living organisms, many of which have therapeutic effects. Pre-, pro-, syn- and post-biotics may beneficially modulate gut microbial composition and function to improve obesity and the aging process. However, the investigation of biotics as next-generation therapeutics has only just begun. Further research is needed to identify therapeutic biotics and understand their mechanisms of action. Investigating the function of the gut-brain axis in obesity and aging may lead to novel therapeutic strategies for obese, aged and comorbid (e.g., sarcopenic obese) patient populations. This review discusses the interrelationship between obesity and aging, with a particular emphasis on the gut microbiome, and presents biotics as novel therapeutic agents for obesity, aging and related disease states.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"4 7","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140964251","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-04-26eCollection Date: 2024-01-01DOI: 10.20517/mrr.2024.04
Marie-Luise Puhlmann, Ember van de Rakt, Evangelia N Kerezoudi, Ignacio Rangel, Robert J Brummer, Hauke Smidt, Frederik S Kaper, Willem M de Vos
Aim: The cell matrix of plant foods has received little attention in prebiotic fiber research. We aimed to understand the impact of the plant cell matrix in dried chicory root on its breakdown in the human gut to explain its reported beneficial effects on gut and metabolic health. Methods: We applied in vitro digestion and fermentation models together with an ex vivo gut barrier integrity model. Plant cell matrix intactness in the upper gastrointestinal tract was investigated by scanning electron microscopy. Colonic breakdown of inulin, and chicory root cubes and powder was assessed by gut microbiota analysis using 16S rRNA gene amplicon sequencing and determining the kinetics of changes in pH, gas, and short-chain fatty acid (SCFA) production. Finally, effects on gut barrier integrity were explored by exposing colonic biopsies to fermentation supernatants in an Ussing chamber model. Results: The plant cell matrix of dried chicory root cubes remained intact throughout upper gastrointestinal transit. Dried chicory root fermentation resulted in higher final relative abundances of pectin-degrading Monoglobus and butyrate-producing Roseburia spp. compared to inulin and a seven-fold increase in Bifidobacterium spp. in donors where these species were present. Dried chicory root cubes yielded similar total SCFAs but higher final butyrate levels than chicory root powder or isolated inulin with less gas produced. No uniform but donor-specific effects of fermentation supernatants on the maintenance of gut barrier integrity were detected. Conclusion: The intact plant cell matrix of dried chicory root affected its colonic breakdown kinetics and microbiota, underpinning its beneficial effect in vivo.
{"title":"Analysis of the fermentation kinetics and gut microbiota modulatory effect of dried chicory root reveals the impact of the plant-cell matrix rationalizing its conversion in the distal colon.","authors":"Marie-Luise Puhlmann, Ember van de Rakt, Evangelia N Kerezoudi, Ignacio Rangel, Robert J Brummer, Hauke Smidt, Frederik S Kaper, Willem M de Vos","doi":"10.20517/mrr.2024.04","DOIUrl":"https://doi.org/10.20517/mrr.2024.04","url":null,"abstract":"<p><p><b>Aim:</b> The cell matrix of plant foods has received little attention in prebiotic fiber research. We aimed to understand the impact of the plant cell matrix in dried chicory root on its breakdown in the human gut to explain its reported beneficial effects on gut and metabolic health. <b>Methods:</b> We applied <i>in vitro</i> digestion and fermentation models together with an <i>ex vivo</i> gut barrier integrity model. Plant cell matrix intactness in the upper gastrointestinal tract was investigated by scanning electron microscopy. Colonic breakdown of inulin, and chicory root cubes and powder was assessed by gut microbiota analysis using 16S rRNA gene amplicon sequencing and determining the kinetics of changes in pH, gas, and short-chain fatty acid (SCFA) production. Finally, effects on gut barrier integrity were explored by exposing colonic biopsies to fermentation supernatants in an Ussing chamber model. <b>Results:</b> The plant cell matrix of dried chicory root cubes remained intact throughout upper gastrointestinal transit. Dried chicory root fermentation resulted in higher final relative abundances of pectin-degrading <i>Monoglobus</i> and butyrate-producing <i>Roseburia</i> spp. compared to inulin and a seven-fold increase in <i>Bifidobacterium</i> spp. in donors where these species were present. Dried chicory root cubes yielded similar total SCFAs but higher final butyrate levels than chicory root powder or isolated inulin with less gas produced. No uniform but donor-specific effects of fermentation supernatants on the maintenance of gut barrier integrity were detected. <b>Conclusion:</b> The intact plant cell matrix of dried chicory root affected its colonic breakdown kinetics and microbiota, underpinning its beneficial effect <i>in vivo</i>.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 3","pages":"28"},"PeriodicalIF":0.0,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11485554/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142485029","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Jennifer Jones, C. Murphy, R. Sleator, E. P. Culligan
Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production. Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7. Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins. Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.
背景：与人类微生物组的其他部分相比，尿液微生物组在健康和疾病中的作用仍是一个研究不足的领域。强化培养技术和下一代测序技术已发现尿生物群是一个尚未开发的潜在新型抗菌素来源。本研究旨在筛选尿液微生物组中编码细菌素生产的基因。研究方法使用细菌素挖掘工具 BAGEL4 和次生代谢物筛选工具 antiSMASH7 对 181 个细菌尿生物群分离物的基因组进行硅学筛选，以确定是否存在细菌素基因簇。结果：从这些分离物中初步确定了 263 个感兴趣的区域，进行了人工标注，并对潜在的细菌素基因簇进行了评估。结果发现 32 个分离物含有 80 个潜在的细菌素基因簇，其中 72% 被鉴定为 II 类细菌素，13.75% 为 III 类细菌素，8.75% 为 I 类细菌素，5% 为未分类细菌素。结论总共发现了 53 种新型变体，包括尼生素、加沙星菌素、琥珀菌素和大肠杆菌素。
{"title":"An exploratory in silico analysis of bacteriocin gene clusters in the urobiome","authors":"Jennifer Jones, C. Murphy, R. Sleator, E. P. Culligan","doi":"10.20517/mrr.2023.78","DOIUrl":"https://doi.org/10.20517/mrr.2023.78","url":null,"abstract":"Background: The role of the urobiome in health and disease remains an understudied area compared to the rest of the human microbiome. Enhanced culturing techniques and next-generation sequencing technologies have identified the urobiome as an untapped source of potentially novel antimicrobials. The aim of this study was to screen the urobiome for genes encoding bacteriocin production.\u0000 Methods: The genomes of 181 bacterial urobiome isolates were screened in silico for the presence of bacteriocin gene clusters using the bacteriocin mining tool BAGEL4 and secondary metabolite screening tool antiSMASH7.\u0000 Results: From these isolates, an initial 263 areas of interest were identified, manually annotated, and evaluated for potential bacteriocin gene clusters. This resulted in 32 isolates containing 80 potential bacteriocin gene clusters, of which 72% were identified as class II, 13.75% as class III, 8.75% as class I, and 5% as unclassified bacteriocins.\u0000 Conclusion: Overall, 53 novel variants were discovered, including nisin, gassericin, ubericin, and colicins.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"47 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140377161","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pilar Manrique, Ignacio Montero, Marta Fernandez-Gosende, Noelia Martinez, Claudio Hidalgo Cantabrana, D. Ríos-Covian
Technological advances in studying the human microbiome in depth have enabled the identification of microbial signatures associated with health and disease. This confirms the crucial role of microbiota in maintaining homeostasis and the host health status. Nowadays, there are several ways to modulate the microbiota composition to effectively improve host health; therefore, the development of therapeutic treatments based on the gut microbiota is experiencing rapid growth. In this review, we summarize the influence of the gut microbiota on the development of infectious disease and cancer, which are two of the main targets of microbiome-based therapies currently being developed. We analyze the two-way interaction between the gut microbiota and traditional drugs in order to emphasize the influence of gut microbial composition on drug effectivity and treatment response. We explore the different strategies currently available for modulating this ecosystem to our benefit, ranging from 1st generation intervention strategies to more complex 2nd generation microbiome-based therapies and their regulatory framework. Lastly, we finish with a quick overview of what we believe is the future of these strategies, that is 3rd generation microbiome-based therapies developed with the use of artificial intelligence (AI) algorithms.
{"title":"Past, present, and future of microbiome-based therapies","authors":"Pilar Manrique, Ignacio Montero, Marta Fernandez-Gosende, Noelia Martinez, Claudio Hidalgo Cantabrana, D. Ríos-Covian","doi":"10.20517/mrr.2023.80","DOIUrl":"https://doi.org/10.20517/mrr.2023.80","url":null,"abstract":"Technological advances in studying the human microbiome in depth have enabled the identification of microbial signatures associated with health and disease. This confirms the crucial role of microbiota in maintaining homeostasis and the host health status. Nowadays, there are several ways to modulate the microbiota composition to effectively improve host health; therefore, the development of therapeutic treatments based on the gut microbiota is experiencing rapid growth. In this review, we summarize the influence of the gut microbiota on the development of infectious disease and cancer, which are two of the main targets of microbiome-based therapies currently being developed. We analyze the two-way interaction between the gut microbiota and traditional drugs in order to emphasize the influence of gut microbial composition on drug effectivity and treatment response. We explore the different strategies currently available for modulating this ecosystem to our benefit, ranging from 1st generation intervention strategies to more complex 2nd generation microbiome-based therapies and their regulatory framework. Lastly, we finish with a quick overview of what we believe is the future of these strategies, that is 3rd generation microbiome-based therapies developed with the use of artificial intelligence (AI) algorithms.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"59 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140232405","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Hypertension, a critical global health concern, is characterized by persistent high blood pressure and is a major cause of cardiovascular events. This perspective explores the multifaceted implications of hypertension, its association with cardiovascular diseases, and the emerging role of the gut microbiota. The gut microbiota, a dynamic community in the gastrointestinal tract, plays a pivotal role in hypertension by influencing blood pressure through the generation of antioxidant, anti-inflammatory, and short-chain fatty acids metabolites, and the conversion of nitrates into nitric oxide. Antihypertensive medications interact with the gut microbiota, impacting drug pharmacokinetics and efficacy. Prebiotics and probiotics present promising avenues for hypertension management, with prebiotics modulating blood pressure through lipid and cholesterol modulation, and probiotics exhibiting a general beneficial effect. Personalized choices based on individual factors are crucial for optimizing prebiotic and probiotic interventions. In conclusion, the gut microbiota’s intricate influence on blood pressure regulation offers innovative perspectives in hypertension therapeutics, with targeted strategies proving valuable for holistic blood pressure management and health promotion.
{"title":"Microbial influence on blood pressure: unraveling the complex relationship for health insights","authors":"Alexander Machado Cardoso","doi":"10.20517/mrr.2023.73","DOIUrl":"https://doi.org/10.20517/mrr.2023.73","url":null,"abstract":"Hypertension, a critical global health concern, is characterized by persistent high blood pressure and is a major cause of cardiovascular events. This perspective explores the multifaceted implications of hypertension, its association with cardiovascular diseases, and the emerging role of the gut microbiota. The gut microbiota, a dynamic community in the gastrointestinal tract, plays a pivotal role in hypertension by influencing blood pressure through the generation of antioxidant, anti-inflammatory, and short-chain fatty acids metabolites, and the conversion of nitrates into nitric oxide. Antihypertensive medications interact with the gut microbiota, impacting drug pharmacokinetics and efficacy. Prebiotics and probiotics present promising avenues for hypertension management, with prebiotics modulating blood pressure through lipid and cholesterol modulation, and probiotics exhibiting a general beneficial effect. Personalized choices based on individual factors are crucial for optimizing prebiotic and probiotic interventions. In conclusion, the gut microbiota’s intricate influence on blood pressure regulation offers innovative perspectives in hypertension therapeutics, with targeted strategies proving valuable for holistic blood pressure management and health promotion.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"46 38","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140231666","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
H. Lai, Lang Yan, Yali Wang, Yuan Mei, Yuli Huang, Xueqing Zeng, Lihong Ge, Jichun Zhao, Yongqing Zhu, Qiaolian Huang, Menglu Yang, Nan Zhao
Aim: Non-salt Suancai is an acidic fermented vegetable consumed by the Chinese Yi ethnic group. Traditionally, it is produced by fermentation without salt in a cold environment. The present study aimed to investigate the metabolite and microbial characteristics, and the effects of substrates/suppliers ingredients on non-salt Suancai. Methods: A simulated fermentation system of non-salt Suancai was constructed by using different substrates/suppliers’ ingredients. The coherence and differential detection of the metabolite and microbial characteristics were done through non-target metabolomic and metagenomic analysis. Results: Lactic acid was the predominant organic acid across all samples. The enumeration of the Lactic acid bacteria showed no discernible differences between study groups, but that of yeast was highest in the mustard leaf stem (Brassica juncea var. latipa ). The three major biological metabolic pathways were metabolism, environmental information, and genetic information processing based on the KEGG database. The metabolite diversity varied with the substrate/supplier of ingredients based on the PLS-DA plot. Lactiplantibacillus , Leuconostoc , and Lactococcus were prevalent in all samples but differentially. The microbial diversity and richness varied significantly, with 36~291 species being identified. Among the various substrates collected from the same supplier, 29, 59, and 29 differential species were identified based on LEfSe [linear discriminant analysis (LDA) > 2, P < 0.05]. Leuconostoc citreum , Leuconostoc mesenteroides , Leuconostoc pseudomesenteroides , Lactiplantibacillus plantarum , and Leuconostoc lactis were likely to be used as the species to discriminate samples collected from different suppliers. Conclusions: This research contributed to the exploration of microbial and metabolite characteristics behind the ingredient restriction of non-salt Suancai using traditional technology.
{"title":"Effects of substrates and suppliers of ingredients on microbial community and metabolites of traditional non-salt Suancai","authors":"H. Lai, Lang Yan, Yali Wang, Yuan Mei, Yuli Huang, Xueqing Zeng, Lihong Ge, Jichun Zhao, Yongqing Zhu, Qiaolian Huang, Menglu Yang, Nan Zhao","doi":"10.20517/mrr.2023.76","DOIUrl":"https://doi.org/10.20517/mrr.2023.76","url":null,"abstract":"Aim: Non-salt Suancai is an acidic fermented vegetable consumed by the Chinese Yi ethnic group. Traditionally, it is produced by fermentation without salt in a cold environment. The present study aimed to investigate the metabolite and microbial characteristics, and the effects of substrates/suppliers ingredients on non-salt Suancai.\u0000 Methods: A simulated fermentation system of non-salt Suancai was constructed by using different substrates/suppliers’ ingredients. The coherence and differential detection of the metabolite and microbial characteristics were done through non-target metabolomic and metagenomic analysis.\u0000 Results: Lactic acid was the predominant organic acid across all samples. The enumeration of the Lactic acid bacteria showed no discernible differences between study groups, but that of yeast was highest in the mustard leaf stem (Brassica juncea var. latipa ). The three major biological metabolic pathways were metabolism, environmental information, and genetic information processing based on the KEGG database. The metabolite diversity varied with the substrate/supplier of ingredients based on the PLS-DA plot. Lactiplantibacillus , Leuconostoc , and Lactococcus were prevalent in all samples but differentially. The microbial diversity and richness varied significantly, with 36~291 species being identified. Among the various substrates collected from the same supplier, 29, 59, and 29 differential species were identified based on LEfSe [linear discriminant analysis (LDA) > 2, P < 0.05]. Leuconostoc citreum , Leuconostoc mesenteroides , Leuconostoc pseudomesenteroides , Lactiplantibacillus plantarum , and Leuconostoc lactis were likely to be used as the species to discriminate samples collected from different suppliers.\u0000 Conclusions: This research contributed to the exploration of microbial and metabolite characteristics behind the ingredient restriction of non-salt Suancai using traditional technology.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"25 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-03-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140247881","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Christine V. Macpherson, Brendan A. Daisley, Elizabeth Mallory, E. Allen-Vercoe
Cell culture is a powerful technique for the investigation of molecular mechanisms fundamental to health and disease in a diverse array of organisms. Cell lines offer several advantages, namely their simplistic approach and high degree of reproducibility. One field where cell culture has proven particularly useful is the study of the microbiome, where cell culture has led to the illumination of microbial influences on host immunity, nutrition, and physiology. Thus far, researchers have focused cell culture work predominantly on humans, but the growing field of insect microbiome research stands to benefit greatly from its application. Insects constitute one of Earth’s most diverse and ancient life forms and, just as with humans, possess microbiomes with great significance to their health. Insects, which play critical roles in supporting food security and ecological stability, are facing increasing threats from agricultural intensification, climate change, and pesticide use. As the microbiome is closely tied to host health, gaining a more robust understanding is of increasing importance. In this review, we assert that the cultivation and utilization of insect gut cell lines in microbiome research will bridge critical knowledge gaps essential for informing insect management practices in a world under pressure.
{"title":"The untapped potential of cell culture in disentangling insect-microbial relationships","authors":"Christine V. Macpherson, Brendan A. Daisley, Elizabeth Mallory, E. Allen-Vercoe","doi":"10.20517/mrr.2023.66","DOIUrl":"https://doi.org/10.20517/mrr.2023.66","url":null,"abstract":"Cell culture is a powerful technique for the investigation of molecular mechanisms fundamental to health and disease in a diverse array of organisms. Cell lines offer several advantages, namely their simplistic approach and high degree of reproducibility. One field where cell culture has proven particularly useful is the study of the microbiome, where cell culture has led to the illumination of microbial influences on host immunity, nutrition, and physiology. Thus far, researchers have focused cell culture work predominantly on humans, but the growing field of insect microbiome research stands to benefit greatly from its application. Insects constitute one of Earth’s most diverse and ancient life forms and, just as with humans, possess microbiomes with great significance to their health. Insects, which play critical roles in supporting food security and ecological stability, are facing increasing threats from agricultural intensification, climate change, and pesticide use. As the microbiome is closely tied to host health, gaining a more robust understanding is of increasing importance. In this review, we assert that the cultivation and utilization of insect gut cell lines in microbiome research will bridge critical knowledge gaps essential for informing insect management practices in a world under pressure.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"85 S1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140411297","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ekaterina Y. Yakovleva, Irina Danilova, Irina Maximova, Alexander Shabaev, Anastasia Dmitrieva, Andrey Belov, Alexandra Klyukina, Ksenia Perfilieva, E. Bonch-Osmolovskaya, Alexander Markov
Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster ) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster . Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster , encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter , potentially beneficial to D. melanogaster , decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia , increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa . This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.
{"title":"Salt concentration in substrate modulates the composition of bacterial and yeast microbiomes of Drosophila melanogaster","authors":"Ekaterina Y. Yakovleva, Irina Danilova, Irina Maximova, Alexander Shabaev, Anastasia Dmitrieva, Andrey Belov, Alexandra Klyukina, Ksenia Perfilieva, E. Bonch-Osmolovskaya, Alexander Markov","doi":"10.20517/mrr.2023.56","DOIUrl":"https://doi.org/10.20517/mrr.2023.56","url":null,"abstract":"Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster ) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster .\u0000 Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster , encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria.\u0000 Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative abundance of Acetobacter , potentially beneficial to D. melanogaster , decreased as NaCl concentration increased, whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%.\u0000 Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia , increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa . This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"46 8","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140419151","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
J. Donkers, Maria Wiese, Tim J. van den Broek, E. Wierenga, Valeria Agamennone, F. Schuren, E. van de Steeg
Background: The gut and its microbiome have a major impact on many aspects of health and are therefore also an attractive target for drug- or food-based therapies. Here, we report on the added value of combining a microbiome screening model, the i-screen, with fresh intestinal tissue explants in a microfluidic gut-on-a-chip model, the Intestinal Explant Barrier Chip (IEBC). Methods: Adult human gut microbiome (fecal pool of 6 healthy donors) was cultured anaerobically in the i-screen platform for 24 h, without and with exposure to 4 mg/mL inulin. The i-screen cell-free culture supernatant was subsequently applied to the luminal side of adult human colon tissue explants (n = 3 donors), fixed in the IEBC, for 24 h and effects were evaluated. Results: The supplementation of the media with inulin promoted the growth of Anaerostipes , Bifidobacterium , Blautia , and Collinsella in the in vitro i-screen, and triggered an elevated production of butyrate by the microbiota. Human colon tissue exposed to inulin-treated i-screen cell-free culture supernatant or control i-screen cell-free culture supernatant with added short-chain fatty acids (SCFAs) showed improved tissue barrier integrity measured by a 28.2%-34.2% reduction in FITC-dextran 4000 (FD4) leakage and 1.3 times lower transport of antipyrine. Furthermore, the release of pro-inflammatory cytokines IL-1β, IL-6, IL-8, and TNF-α was reduced under these circumstances. Gene expression profiles confirmed these findings, but showed more profound effects for inulin-treated supernatant compared to SCFA-supplemented supernatant. Conclusion: The combination of i-screen and IEBC facilitates the study of complex intestinal processes such as host-microbial metabolite interaction and gut health.
{"title":"A host-microbial metabolite interaction gut-on-a-chip model of the adult human intestine demonstrates beneficial effects upon inulin treatment of gut microbiome","authors":"J. Donkers, Maria Wiese, Tim J. van den Broek, E. Wierenga, Valeria Agamennone, F. Schuren, E. van de Steeg","doi":"10.20517/mrr.2023.79","DOIUrl":"https://doi.org/10.20517/mrr.2023.79","url":null,"abstract":"Background: The gut and its microbiome have a major impact on many aspects of health and are therefore also an attractive target for drug- or food-based therapies. Here, we report on the added value of combining a microbiome screening model, the i-screen, with fresh intestinal tissue explants in a microfluidic gut-on-a-chip model, the Intestinal Explant Barrier Chip (IEBC).\u0000 Methods: Adult human gut microbiome (fecal pool of 6 healthy donors) was cultured anaerobically in the i-screen platform for 24 h, without and with exposure to 4 mg/mL inulin. The i-screen cell-free culture supernatant was subsequently applied to the luminal side of adult human colon tissue explants (n = 3 donors), fixed in the IEBC, for 24 h and effects were evaluated.\u0000 Results: The supplementation of the media with inulin promoted the growth of Anaerostipes , Bifidobacterium , Blautia , and Collinsella in the in vitro i-screen, and triggered an elevated production of butyrate by the microbiota. Human colon tissue exposed to inulin-treated i-screen cell-free culture supernatant or control i-screen cell-free culture supernatant with added short-chain fatty acids (SCFAs) showed improved tissue barrier integrity measured by a 28.2%-34.2% reduction in FITC-dextran 4000 (FD4) leakage and 1.3 times lower transport of antipyrine. Furthermore, the release of pro-inflammatory cytokines IL-1β, IL-6, IL-8, and TNF-α was reduced under these circumstances. Gene expression profiles confirmed these findings, but showed more profound effects for inulin-treated supernatant compared to SCFA-supplemented supernatant.\u0000 Conclusion: The combination of i-screen and IEBC facilitates the study of complex intestinal processes such as host-microbial metabolite interaction and gut health.","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"5 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-02-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140439234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Population aging is a substantial challenge for the global sanitation framework. Unhealthy aging tends to be accompanied by chronic diseases such as cardiovascular disease, diabetes, and cancer, which undermine the welfare of the elderly. Based on the fact that aging is inevitable but retarding aging is attainable, flexible aging characterization and efficient anti-aging become imperative for healthy aging. The gut microbiome, as the most dynamic component interacting with the organism, can affect the aging process through its own structure and metabolites, thus holding the potential to become both an ideal aging-related biomarker and an intervention strategy. This review summarizes the value of applying gut microbiota as aging-related microbial biomarkers in diagnosing aging state and monitoring the effect of anti-aging interventions, ultimately pointing to the future prospects of microbial intervention strategies in maintaining healthy aging.
{"title":"Gut microbiota: an ideal biomarker and intervention strategy for aging.","authors":"Xuan Xu, Tangchang Xu, Jing Wei, Tingtao Chen","doi":"10.20517/mrr.2023.68","DOIUrl":"10.20517/mrr.2023.68","url":null,"abstract":"<p><p>Population aging is a substantial challenge for the global sanitation framework. Unhealthy aging tends to be accompanied by chronic diseases such as cardiovascular disease, diabetes, and cancer, which undermine the welfare of the elderly. Based on the fact that aging is inevitable but retarding aging is attainable, flexible aging characterization and efficient anti-aging become imperative for healthy aging. The gut microbiome, as the most dynamic component interacting with the organism, can affect the aging process through its own structure and metabolites, thus holding the potential to become both an ideal aging-related biomarker and an intervention strategy. This review summarizes the value of applying gut microbiota as aging-related microbial biomarkers in diagnosing aging state and monitoring the effect of anti-aging interventions, ultimately pointing to the future prospects of microbial intervention strategies in maintaining healthy aging.</p>","PeriodicalId":94376,"journal":{"name":"Microbiome research reports","volume":"3 2","pages":"13"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149087/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141263412","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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