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Feitosa-Junior OR, Lubbe A, Kosina SM, Martins-Junior J, Barbosa D, Baccari C, Zaini PA, Bowen BP, Northen TR, Lindow SE, da Silva AM. The Exometabolome of Xylella fastidiosa in Contact with Paraburkholderia phytofirmans Supernatant Reveals Changes in Nicotinamide, Amino Acids, Biotin, and Plant Hormones. Metabolites 2024; 14:82. [PMID: 38392974 PMCID: PMC10890622 DOI: 10.3390/metabo14020082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/11/2024] [Accepted: 01/12/2024] [Indexed: 02/25/2024] Open
Abstract
Microbial competition within plant tissues affects invading pathogens' fitness. Metabolomics is a great tool for studying their biochemical interactions by identifying accumulated metabolites. Xylella fastidiosa, a Gram-negative bacterium causing Pierce's disease (PD) in grapevines, secretes various virulence factors including cell wall-degrading enzymes, adhesion proteins, and quorum-sensing molecules. These factors, along with outer membrane vesicles, contribute to its pathogenicity. Previous studies demonstrated that co-inoculating X. fastidiosa with the Paraburkholderia phytofirmans strain PsJN suppressed PD symptoms. Here, we further investigated the interaction between the phytopathogen and the endophyte by analyzing the exometabolome of wild-type X. fastidiosa and a diffusible signaling factor (DSF) mutant lacking quorum sensing, cultivated with 20% P. phytofirmans spent media. Liquid chromatography-mass spectrometry (LC-MS) and the Method for Metabolite Annotation and Gene Integration (MAGI) were used to detect and map metabolites to genomes, revealing a total of 121 metabolites, of which 25 were further investigated. These metabolites potentially relate to host adaptation, virulence, and pathogenicity. Notably, this study presents the first comprehensive profile of X. fastidiosa in the presence of a P. phytofirmans spent media. The results highlight that P. phytofirmans and the absence of functional quorum sensing affect the ratios of glutamine to glutamate (Gln:Glu) in X. fastidiosa. Additionally, two compounds with plant metabolism and growth properties, 2-aminoisobutyric acid and gibberellic acid, were downregulated when X. fastidiosa interacted with P. phytofirmans. These findings suggest that P. phytofirmans-mediated disease suppression involves modulation of the exometabolome of X. fastidiosa, impacting plant immunity.
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Affiliation(s)
- Oseias R Feitosa-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Andrea Lubbe
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Suzanne M Kosina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joaquim Martins-Junior
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Deibs Barbosa
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
| | - Clelia Baccari
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Paulo A Zaini
- Department of Plant Sciences, University of California, Davis, CA 95616, USA
| | - Benjamin P Bowen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Trent R Northen
- The DOE Joint Genome Institute, Berkeley, CA 94720, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | - Aline M da Silva
- Department of Biochemistry, Institute of Chemistry, University of Sao Paulo, Sao Paulo 05508-900, SP, Brazil
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2
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Gao X, Zhao J, Chen W, Zhai Q. Food and drug design for gut microbiota-directed regulation: Current experimental landscape and future innovation. Pharmacol Res 2023; 194:106867. [PMID: 37499703 DOI: 10.1016/j.phrs.2023.106867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 07/19/2023] [Accepted: 07/23/2023] [Indexed: 07/29/2023]
Abstract
Most diets and medications enhance host health via microbiota-dependent ways, but it is in the present situation of untargeted regulation. Non-targeted regulation may lead to the ineffectiveness of dietary supplements or drug treatment. Microbiota-directed food, aiming to improve diseases by targeting specific microbes without affecting other bacteria, have been proposed to deal with this problem. However, there is currently no universally applicable method to explore such foods or drugs. In this review, thirty studies on recent efforts in microbiota directed diets and medications are summarized from various databases. The methods used to find new foods and medications are primarily divided into four groups depending on the experimental models: in vivo and in vitro, as well as predictions based on bioinformatics. We also discuss their implementation, interpretation, and respective limitations, and describe the present situation. We further put forward a framework for microbiota-directed foods and medicine according to above methods and other microbiome manipulation, which will spur precision medicine.
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Affiliation(s)
- Xiaoxiang Gao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Resources, Jiangnan University, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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3
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Kussmann M, Abe Cunha DH, Berciano S. Bioactive compounds for human and planetary health. Front Nutr 2023; 10:1193848. [PMID: 37545571 PMCID: PMC10400358 DOI: 10.3389/fnut.2023.1193848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Accepted: 06/15/2023] [Indexed: 08/08/2023] Open
Abstract
Bioactive compounds found in edible plants and foods are vital for human and planetary health, yet their significance remains underappreciated. These natural bioactives, as part of whole diets, ingredients, or supplements, can modulate multiple aspects of human health and wellness. Recent advancements in omic sciences and computational biology, combined with the development of Precision Nutrition, have contributed to the convergence of nutrition and medicine, as well as more efficient and affordable healthcare solutions that harness the power of food for prevention and therapy. Innovation in this field is crucial to feed a growing global population sustainably and healthily. This requires significant changes in our food system, spanning agriculture, production, distribution and consumption. As we are facing pressing planetary health challenges, investing in bioactive-based solutions is an opportunity to protect biodiversity and the health of our soils, waters, and the atmosphere, while also creating value for consumers, patients, communities, and stakeholders. Such research and innovation targets include alternative proteins, such as cellular agriculture and plant-derived protein; natural extracts that improve shelf-life as natural preservatives; upcycling of agricultural by-products to reduce food waste; and the development of natural alternatives to synthetic fertilizers and pesticides. Translational research and innovation in the field of natural bioactives are currently being developed at two levels, using a systems-oriented approach. First, at the biological level, the interplay between these compounds and the human host and microbiome is being elucidated through omics research, big data and artificial intelligence, to accelerate both discovery and validation. Second, at the ecosystem level, efforts are focused on producing diverse nutrient-rich, flavorful, and resilient, yet high-yield agricultural crops, and educating consumers to make informed choices that benefit both their health and the planet. Adopting a system-oriented perspective helps: unravel the intricate and dynamic relationships between bioactives, nutrition, and sustainability outcomes, harnessing the power of nature to promote human health and wellbeing; foster sustainable agriculture and protect the ecosystem. Interdisciplinary collaboration in this field is needed for a new era of research and development of practical food-based solutions for some of the most pressing challenges humanity and our planet are facing today.
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Affiliation(s)
- Martin Kussmann
- Kompetenzzentrum für Ernährung (KErn), Freising, Germany
- Kussmann Biotech GmbH, Nordkirchen, Germany
| | - David Henrique Abe Cunha
- Ideatomik Creative Industries, Botucatu, Brazil
- Institute of Biosciences, São Paulo State University, Rio Claro, Brazil
| | - Silvia Berciano
- Friedman School of Nutrition Science and Policy, Tufts University, Boston, MA, United States
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4
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Gao X, Yue C, Tian R, Yu L, Tian F, Zhao J, Chen W, Zhai Q. The regulatory effects of specific polyphenols on Akkermansia are dependent on uridine. Food Chem 2023; 410:135367. [PMID: 36610089 DOI: 10.1016/j.foodchem.2022.135367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 12/31/2022]
Abstract
We examined the microbial regulatory capacity of four polyphenols with different structure in healthy mice and explore the mechanism according to exogenous metabolites and microbial metabolites. Oral administration of four polyphenols, including caffeic acid (CA), procyanidin (PA), puerarin (Pue), and resveratrol (Res), did not lead to metabolic disorder in healthy mice. Gut microbiota analysis revealed that CA, PA, and Pue administration significantly enhanced the abundance of Akkermansia and Ruminococcaceae UCG-014 while Res supplement mainly promoted the growth of Lactobacillus and Bacteroides. Furthermore, correlation analysis and exogenous metabolite prediction revealed that the effects of polyphenols, including CA, PA, and Pue, on Akkermansia have strong relationship with uridine while the regulation of Res on microbiota might be dependent on the decrease on petroselinic acid. These investigations considerably suggest the importance of exploration of exogenous metabolites and reveal the similarity of effects of polyphenols on microbiota and metabolites.
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Affiliation(s)
- Xiaoxiang Gao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Chenbo Yue
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Ruocen Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Leilei Yu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Fengwei Tian
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; National Engineering Research Center for Functional Food, Jiangnan University, Wuxi, Jiangsu 214122, China
| | - Qixiao Zhai
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China; School of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu 214122, China.
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5
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Plaza-Diaz J, Ruiz-Ojeda FJ, Morales J, Martín-Masot R, Climent E, Silva Á, Martinez-Blanch JF, Enrique M, Tortajada M, Ramon D, Alvarez B, Chenoll E, Gil Á. Innova 2020: A Follow-Up Study of the Fecal Microbiota of Infants Using a Novel Infant Formula between 6 Months and 12 Months of Age. Int J Mol Sci 2023; 24:7392. [PMID: 37108555 PMCID: PMC10139017 DOI: 10.3390/ijms24087392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/10/2023] [Accepted: 04/16/2023] [Indexed: 04/29/2023] Open
Abstract
The World Health Organization recommends exclusive breastfeeding on demand until at least the sixth month of life. Breast milk or infant formula is the infant's primary food source until the age of one year, followed by the gradual introduction of other foods. During weaning, the intestinal microbiota evolves to a profile close to that of the adult, and its disruption can result in an increased incidence of acute infectious diseases. We aimed to determine whether a novel starting formula (INN) provides gut microbiota compositions more similar to those of breastfed (BF) infants from 6 to 12 months of age compared to a standard formula (STD). This study included 210 infants (70 per group) who completed the intervention until they reached the age of 12 months. In the intervention period, infants were divided into three groups. Group 1 received an INN formula with a lower protein content, a casein to whey protein ratio of approximately 70/30, twice as much docosahexaenoic acid as the STD formula, a thermally inactivated postbiotic (Bifidobacterium animalis subsp. lactis, BPL1TM HT), and twice as much arachidonic acid as the STD formula contained. The second group received the STD formula, while the third group was exclusively BF for exploratory purposes. In the course of the study, visits were conducted at 6 months and 12 months of age. Compared to the BF and STD groups, the Bacillota phylum levels in the INN group were significantly reduced after 6 months. At the end of 6 months, the alpha diversity indices of the BF and INN groups differed significantly from those of the STD group. At 12 months, the Verrucomicrobiota phylum levels in the STD group were significantly lower than those in the BF and INN groups. Based on the comparison between 6 and 12 months, the Bacteroidota phylum levels in the BF group were significantly higher than those in the INN and STD groups. When comparing the INN group with the BF and STD groups, Clostridium sensu stricto 1 was significantly higher in the INN group. The STD group had higher levels of calprotectin than the INN and BF groups at 6 months. The immunoglobulin A levels in the STD group were significantly lower than those in the INN and BF groups after 6 months. Both formulas had significantly higher levels of propionic acid than the BF group at 6 months. At 6 months, the STD group showed a higher quantification of all metabolic pathways than the BF group. The INN formula group exhibited similar behavior to the BF group, except for the superpathway of phospholipid biosynthesis (E. coli). We hypothesize that the novel INN formula may promote an intestinal microbiota that is more similar to the microbiota of an infant who consumes only human milk before the weaning period.
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Affiliation(s)
- Julio Plaza-Diaz
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- Children’s Hospital of Eastern Ontario Research Institute, Ottawa, ON K1H 8L1, Canada
| | - Francisco Javier Ruiz-Ojeda
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764 Munich, Germany
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n. Armilla, 18016 Granada, Spain
| | - Javier Morales
- Product Development Department, Alter Farmacia SA, 28880 Madrid, Spain
| | - Rafael Martín-Masot
- Institute of Nutrition and Food Technology “José Mataix”, Centre of Biomedical Research, University of Granada, Avda. del Conocimiento s/n. Armilla, 18016 Granada, Spain
- Pediatric Gastroenterology and Nutrition Unit, Hospital Regional Universitario de Málaga, 29010 Málaga, Spain
| | - Eric Climent
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Ángela Silva
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | | | - María Enrique
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Marta Tortajada
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Daniel Ramon
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Beatriz Alvarez
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Empar Chenoll
- ADM-BIOPOLIS, Scientific Park Universitat de València, 46980 València, Spain
| | - Ángel Gil
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada, 18071 Granada, Spain
- Instituto de Investigación Biosanitaria IBS.GRANADA, Complejo Hospitalario Universitario de Granada, 18014 Granada, Spain
- RG Adipocytes and Metabolism, Institute for Diabetes and Obesity, Helmholtz Diabetes Center at Helmholtz Center Munich, Neuherberg, 85764 Munich, Germany
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, 28029 Madrid, Spain
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6
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Jia Y, Wang P, Ou Y, Yan Y, Zhou S, Sun L, Lu H. Insights into the microbial response mechanisms to ciprofloxacin during sulfur-mediated biological wastewater treatment using a metagenomics approach. Water Res 2022; 223:118995. [PMID: 36007398 DOI: 10.1016/j.watres.2022.118995] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 06/15/2023]
Abstract
The fate and removal of ciprofloxacin, a class of fluoroquinolone antibiotic, during sulfur-mediated biological wastewater treatment has been recently well documented. However, little is known regarding the genetic response of microorganisms to ciprofloxacin. Here, a lab-scale anaerobic sulfate-reducing bioreactor was continuously operated over a long term for ciprofloxacin-contaminated wastewater treatment to investigate the response of the microorganisms to ciprofloxacin by adopting a metagenomics approach. It was found that total organic carbon (TOC) removal and sulfate reduction were promoted by approximately 10% under ciprofloxacin stress, along with the enrichment of functional genera (e.g., Desulfobacter, Geobacter) involved in carbon and sulfur metabolism. The metagenomic analytical results demonstrated that ciprofloxacin triggered the microbial SOS response, as demonstrated by the up-regulation of the multidrug efflux pump genes (8-125-fold higher than that of the control) and ciprofloxacin-degrading genes (4-33-fold higher than that of the control). Moreover, the contents of ATP, NADH, and cytochrome C, as well as related functional genes (including genes involved in energy generation, electron transport, carbon metabolism, and sulfur metabolism) were markedly increased under ciprofloxacin stress. This demonstrated that the carbon and sulfur metabolisms were enhanced for energy (ATP) generation and electron transport in response to ciprofloxacin-induced stress. Interestingly, the microbes tended to cooperate while being subjected exposure to exogenous ciprofloxacin according to the reconstructed metabolic network using the NetSeed model. Particularly, the species with higher complementarity indices played more pivotal roles in strengthening microbial metabolism and the SOS response under long-term ciprofloxacin stress. This study characterized the response mechanisms of microorganisms to ciprofloxacin at the genetic level in sulfur-mediated biological wastewater treatment. These new understandings will contribute the scientific basis for improving and optimizing the sulfur-mediated bioprocess for antibiotics-laden wastewater treatment.
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Affiliation(s)
- Yanyan Jia
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Pandeng Wang
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Yuyi Ou
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Yujian Yan
- School of Ecology, Sun Yat-sen University, Guangzhou, PR China
| | - Sining Zhou
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Lianpeng Sun
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China
| | - Hui Lu
- School of Environmental Science and Engineering, Sun Yat-sen University, Guangzhou, PR China; Guangdong Provincial Key Laboratory of Environmental Pollution Control and Remediation Technology (Sun Yat-sen University), Guangzhou, PR China.
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Abstract
Antibiotics have become a mainstay of healthcare in the past century due to their activity against pathogens. This manuscript reviews the impact of antibiotic use on the intestinal microbiota in the context of mass drug administration (MDA). The importance of the gut microbiota to human metabolism and physiology is now well established, and antibiotic exposure may impact host health via collateral effects on the microbiota and its functions. To gain further insight into how gut microbiota respond to antibiotic perturbation and the implications for public health, factors that influence the impact of antibiotic exposure on the microbiota, potential health outcomes of antibiotic-induced microbiota alterations, and strategies that have the potential to ameliorate these wider antibiotic-associated microbiota perturbations are also reviewed.
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Affiliation(s)
- Ethan K Gough
- Department of International Health, Human Nutrition Program, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
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8
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Silva Gonçalves O, Bonandi Barreiros R, Martins Tupy S, Ferreira Santana M. A reverse-ecology framework to uncover the potential metabolic interplay among 'Candidatus Liberibacter' species, Citrus hosts and psyllid vector. Gene X 2022; 837:146679. [PMID: 35752379 DOI: 10.1016/j.gene.2022.146679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 05/31/2022] [Accepted: 06/10/2022] [Indexed: 11/04/2022] Open
Abstract
'Candidatus Liberibacter' species have developed a dependency on essential nutrients and metabolites from the host cell, as a result of substantial genome reduction. Still, it is difficult to state which nutrients they acquire and whether or not they are metabolically reliant. We used a reverse-ecology model to investigate the potential metabolic interactions of 'Ca Liberibacter' species, Citrus, and the psyllid Diaphorina citri in the huanglongbing disease pyramid. Our findings show that hosts (citrus and psyllid) tend to support the nutritional needs of 'Ca. Liberibacter' species, implying that the pathogen's metabolism has become tightly linked to hosts, which may reflect in the parasite lifestyle of this important genus.
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Affiliation(s)
- Osiel Silva Gonçalves
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Ralph Bonandi Barreiros
- Departmento de Fitotecnia, Laboratório de Biotecnologia de Plantas Horticulas, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, Brazil
| | - Sumaya Martins Tupy
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil
| | - Mateus Ferreira Santana
- Grupo de Genômica Evolutiva Microbiana, Laboratório de Genética Molecular de Microrganismos, Departamento de Microbiologia, Instituto de Biotecnologia Aplicada à Agropecuária, Universidade Federal de Viçosa, Minas Gerais, Brazil.
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9
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Lovell AL, Eriksen H, McKeen S, Mullaney J, Young W, Fraser K, Altermann E, Gasser O, Kussmann M, Roy NC, McNabb WC, Wall CR. "Nourish to Flourish": complementary feeding for a healthy infant gut microbiome-a non-randomised pilot feasibility study. Pilot Feasibility Stud 2022; 8:103. [PMID: 35585649 PMCID: PMC9116017 DOI: 10.1186/s40814-022-01059-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/03/2022] [Indexed: 11/10/2022] Open
Abstract
Background The introduction of complementary foods and changes in milk feeding result in modifications to gastrointestinal function. The interplay between indigestible carbohydrates, host physiology, and microbiome, and immune system development are areas of intense research relevant to early and later-life health. Methods This 6-month prospective non-randomised feasibility study was conducted in Auckland, New Zealand (NZ), in January 2018. Forty parents/caregivers and their infants were enrolled, with 30 infants allocated to receive a prebiotic NZ kūmara (flesh and skin; a type of sweet potato) prepared as a freeze-dried powder, and ten infants allocated to receive a commercially available probiotic control known to show relevant immune benefits (109 CFU Bifidobacterium lactis BB-12®). The primary outcome was the study feasibility measures which are reported here. Results Recruitment, participant retention, and data collection met feasibility targets. Some limitations to biological sample collection were encountered, with difficulties in obtaining sufficient plasma sample volumes for the proposed immune parameter analyses. Acceptability of the kūmara powder was met with no reported adverse events. Conclusion This study indicates that recruiting infants before introducing complementary foods is feasible, with acceptable adherence to the food-based intervention. These results will inform the protocol of a full-scale randomised controlled trial (RCT) with adjustments to the collection of biological samples to examine the effect of a prebiotic food on the prevalence of respiratory tract infections during infancy. Trial registration Australia New Zealand Clinical Trials Registry ACTRN12618000157279. Prospectively registered on 02/01/2018. Supplementary Information The online version contains supplementary material available at 10.1186/s40814-022-01059-3.
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Affiliation(s)
- Amy L Lovell
- Department of Nutrition and Dietetics, The University of Auckland Faculty of Medical and Health Sciences, Private Bag 92019, Auckland, 1142, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Hannah Eriksen
- Department of Nutrition and Dietetics, The University of Auckland Faculty of Medical and Health Sciences, Private Bag 92019, Auckland, 1142, New Zealand.,High-Value Nutrition National Science Challenge, Auckland, New Zealand
| | - Starin McKeen
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,AgResearch Ltd. Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Jane Mullaney
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,AgResearch Ltd. Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Wayne Young
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,AgResearch Ltd. Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Karl Fraser
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,AgResearch Ltd. Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Eric Altermann
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,AgResearch Ltd. Grasslands Research Centre, Private Bag 11008, Palmerston North, 4442, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Olivier Gasser
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Malaghan Institute of Medical Research, PO Box 7060, Newtown, Wellington, 6242, New Zealand
| | | | - Nicole C Roy
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,University of Otago, PO Box 56, Dunedin, 9054, New Zealand
| | - Warren C McNabb
- High-Value Nutrition National Science Challenge, Auckland, New Zealand.,Riddet Institute, Massey University, Private Bag 11222, Palmerston North, 4442, New Zealand
| | - Clare R Wall
- Department of Nutrition and Dietetics, The University of Auckland Faculty of Medical and Health Sciences, Private Bag 92019, Auckland, 1142, New Zealand. .,High-Value Nutrition National Science Challenge, Auckland, New Zealand.
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10
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Bauermeister A, Mannochio-Russo H, Costa-Lotufo LV, Jarmusch AK, Dorrestein PC. Mass spectrometry-based metabolomics in microbiome investigations. Nat Rev Microbiol 2022; 20:143-160. [PMID: 34552265 PMCID: PMC9578303 DOI: 10.1038/s41579-021-00621-9] [Citation(s) in RCA: 115] [Impact Index Per Article: 57.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Microbiotas are a malleable part of ecosystems, including the human ecosystem. Microorganisms affect not only the chemistry of their specific niche, such as the human gut, but also the chemistry of distant environments, such as other parts of the body. Mass spectrometry-based metabolomics is one of the key technologies to detect and identify the small molecules produced by the human microbiota, and to understand the functional role of these microbial metabolites. This Review provides a foundational introduction to common forms of untargeted mass spectrometry and the types of data that can be obtained in the context of microbiome analysis. Data analysis remains an obstacle; therefore, the emphasis is placed on data analysis approaches and integrative analysis, including the integration of microbiome sequencing data.
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Affiliation(s)
- Anelize Bauermeister
- Institute of Biomedical Science, Universidade de São Paulo, São Paulo, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Helena Mannochio-Russo
- Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University, Araraquara, SP, Brazil,Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | | | - Alan K. Jarmusch
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, CA, USA.,Department of Pediatrics, University of California, San Diego, CA, USA.,Center for Microbiome Innovation, University of California, San Diego, CA, USA
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11
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Salekeen R, Siam MHB, Sharif DI, Lustgarten MS, Billah MM, Islam KMD. In silico insights into potential gut microbial modulation of NAD+ metabolism and longevity. J Biochem Mol Toxicol 2021; 35:e22925. [PMID: 34580953 DOI: 10.1002/jbt.22925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 11/08/2022]
Abstract
Recent evidence has prompted the notion of gut-microbial signatures as an indirect marker of aging and aging-associated decline in humans. However, the underlying host-symbiont molecular interactions contributing to these signatures remain poorly understood. In this study, we address this gap using cheminformatic analyses to elucidate potential gut microbial metabolites that may perturb the longevity-associated NAD+ metabolic network. In silico ADMET, KEGG interaction analysis, molecular docking, molecular dynamics simulation, and molecular mechanics calculation predict a large number of safe and bioavailable microbial metabolites to be direct and/or indirect activators of NAD+-dependent sirtuin proteins. Our simulation results suggest dihydropteroate, phenylpyruvic acid, indole-3-propionic acid, phenyllactic acid, all-trans-retinoic acid, and multiple deoxy-, methyl-, and cyclic nucleotides from intestinal microbiota as the best-performing regulators of NAD+ metabolism. Retracing these molecules to their source microorganisms also suggest commensal Escherichia, Bacteroides, Bifidobacteria, and Lactobacilli to be associated with the highest number of pro-longevity metabolites. These findings from our early-stage study, therefore, provide an informatics-based context for previous evidence in the area and grant novel insights for future clinical investigation intersecting anti-aging drug discovery, probiotics, and gut microbial signatures.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Md Hasanul Banna Siam
- Department of Microbiology, Faculty of Biological Science, University of Dhaka, Dhaka, Bangladesh
| | - Dilara Islam Sharif
- Department of Genetic Engineering and Biotechnology, Faculty of Life and Earth Sciences, Jagannath University, Dhaka, Bangladesh
| | - Michael S Lustgarten
- Nutrition, Exercise Physiology, and Sarcopenia Laboratory, Jean Mayer USDA Human Nutrition Research Center, Tufts University, Boston, Massachusetts, USA
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh
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12
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Parolo S, Tomasoni D, Bora P, Ramponi A, Kaddi C, Azer K, Domenici E, Neves-Zaph S, Lombardo R. Reconstruction of the Cytokine Signaling in Lysosomal Storage Diseases by Literature Mining and Network Analysis. Front Cell Dev Biol 2021; 9:703489. [PMID: 34490253 PMCID: PMC8417786 DOI: 10.3389/fcell.2021.703489] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/30/2021] [Indexed: 11/13/2022] Open
Abstract
Lysosomal storage diseases (LSDs) are characterized by the abnormal accumulation of substrates in tissues due to the deficiency of lysosomal proteins. Among the numerous clinical manifestations, chronic inflammation has been consistently reported for several LSDs. However, the molecular mechanisms involved in the inflammatory response are still not completely understood. In this study, we performed text-mining and systems biology analyses to investigate the inflammatory signals in three LSDs characterized by sphingolipid accumulation: Gaucher disease, Acid Sphingomyelinase Deficiency (ASMD), and Fabry Disease. We first identified the cytokines linked to the LSDs, and then built on the extracted knowledge to investigate the inflammatory signals. We found numerous transcription factors that are putative regulators of cytokine expression in a cell-specific context, such as the signaling axes controlled by STAT2, JUN, and NR4A2 as candidate regulators of the monocyte Gaucher disease cytokine network. Overall, our results suggest the presence of a complex inflammatory signaling in LSDs involving many cellular and molecular players that could be further investigated as putative targets of anti-inflammatory therapies.
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Affiliation(s)
- Silvia Parolo
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
| | - Danilo Tomasoni
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
| | - Pranami Bora
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
| | - Alan Ramponi
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
| | - Chanchala Kaddi
- Data and Data Science - Translational Disease Modeling, Sanofi, Bridgewater, NJ, United States
| | - Karim Azer
- Data and Data Science - Translational Disease Modeling, Sanofi, Bridgewater, NJ, United States
| | - Enrico Domenici
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy.,Department of Cellular, Computational and Integrative Biology (CIBIO), University of Trento, Trento, Italy
| | - Susana Neves-Zaph
- Data and Data Science - Translational Disease Modeling, Sanofi, Bridgewater, NJ, United States
| | - Rosario Lombardo
- Fondazione the Microsoft Research-University of Trento Centre for Computational and Systems Biology, Rovereto, Italy
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13
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Azer K, Kaddi CD, Barrett JS, Bai JPF, McQuade ST, Merrill NJ, Piccoli B, Neves-Zaph S, Marchetti L, Lombardo R, Parolo S, Immanuel SRC, Baliga NS. History and Future Perspectives on the Discipline of Quantitative Systems Pharmacology Modeling and Its Applications. Front Physiol 2021; 12:637999. [PMID: 33841175 PMCID: PMC8027332 DOI: 10.3389/fphys.2021.637999] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/25/2021] [Indexed: 12/24/2022] Open
Abstract
Mathematical biology and pharmacology models have a long and rich history in the fields of medicine and physiology, impacting our understanding of disease mechanisms and the development of novel therapeutics. With an increased focus on the pharmacology application of system models and the advances in data science spanning mechanistic and empirical approaches, there is a significant opportunity and promise to leverage these advancements to enhance the development and application of the systems pharmacology field. In this paper, we will review milestones in the evolution of mathematical biology and pharmacology models, highlight some of the gaps and challenges in developing and applying systems pharmacology models, and provide a vision for an integrated strategy that leverages advances in adjacent fields to overcome these challenges.
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Affiliation(s)
- Karim Azer
- Quantitative Sciences, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, United States
| | - Chanchala D. Kaddi
- Quantitative Sciences, Bill and Melinda Gates Medical Research Institute, Cambridge, MA, United States
| | | | - Jane P. F. Bai
- Office of Clinical Pharmacology, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Sean T. McQuade
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Nathaniel J. Merrill
- Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Benedetto Piccoli
- Department of Mathematical Sciences and Center for Computational and Integrative Biology, Rutgers University, Camden, NJ, United States
| | - Susana Neves-Zaph
- Translational Disease Modeling, Data and Data Science, Sanofi, Bridgewater, NJ, United States
| | - Luca Marchetti
- Fondazione the Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Rosario Lombardo
- Fondazione the Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
| | - Silvia Parolo
- Fondazione the Microsoft Research – University of Trento Centre for Computational and Systems Biology (COSBI), Rovereto, Italy
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14
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Seol D, Jhang SY, Kim H, Kim SY, Kwak HS, Kim SH, Lee W, Park S, Kim H, Cho S, Kwak W. Accurate and Strict Identification of Probiotic Species Based on Coverage of Whole-Metagenome Shotgun Sequencing Data. Front Microbiol 2019; 10:1683. [PMID: 31440213 PMCID: PMC6693478 DOI: 10.3389/fmicb.2019.01683] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Accepted: 07/08/2019] [Indexed: 11/13/2022] Open
Abstract
Identifying the microbes present in probiotic products is an important issue in product quality control and public health. The most common methods used to identify genera containing species that produce lactic acid are matrix-assisted laser desorption/ionization–time of flight mass spectrometry (MALDI-TOF MS) and 16S rRNA sequence analysis. However, the high cost of operation, difficulty in distinguishing between similar species, and limitations of the current sequencing technologies have made it difficult to obtain accurate results using these tools. To overcome these problems, a whole-genome shotgun sequencing approach has been developed along with various metagenomic classification tools. Widely used tools include the marker gene and k-mer methods, but their inevitable false-positives (FPs) hampered an accurate analysis. We therefore, designed a coverage-based pipeline to reduce the FP problem and to achieve a more reliable identification of species. The coverage-based pipeline described here not only shows higher accuracy for the detection of species and proportion analysis, based on mapping depth, but can be applied regardless of the sequencing platform. We believe that the coverage-based pipeline described in this study can provide appropriate support for probiotic quality control, addressing current labeling issues.
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Affiliation(s)
- Donghyeok Seol
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - So Yun Jhang
- C&K Genomics, Songpa-gu, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Hyaekang Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Se-Young Kim
- R&D Center, CTCBIO, Inc., Hwaseong-si, South Korea
| | - Hyo-Sun Kwak
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Soon Han Kim
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Woojung Lee
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Sewook Park
- Division of Microbiology, Ministry of Food and Drug Safety, Cheongju-si, South Korea
| | - Heebal Kim
- C&K Genomics, Songpa-gu, South Korea.,Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, South Korea
| | - Seoae Cho
- C&K Genomics, Songpa-gu, South Korea
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