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Yang Y, Hu R, Wang W, Zhang T. Construction and optimization of non-parametric analysis model for meter coefficients via back propagation neural network. Sci Rep 2024; 14:11452. [PMID: 38769323 PMCID: PMC11106294 DOI: 10.1038/s41598-024-61702-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Accepted: 05/08/2024] [Indexed: 05/22/2024] Open
Abstract
This study addresses the drawbacks of traditional methods used in meter coefficient analysis, which are low accuracy and long processing time. A new method based on non-parametric analysis using the Back Propagation (BP) neural network is proposed to overcome these limitations. The study explores the classification and pattern recognition capabilities of the BP neural network by analyzing its non-parametric model and optimization methods. For model construction, the study uses the United Kingdom Domestic Appliance-Level Electricity dataset's meter readings and related data for training and testing the proposed model. The non-parametric analysis model is used for data pre-processing, feature extraction, and normalization to obtain the training and testing datasets. Experimental tests compare the proposed non-parametric analysis model based on the BP neural network with the traditional Least Squares Method (LSM). The results demonstrate that the proposed model significantly improves the accuracy indicators such as mean absolute error (MAE) and mean relative error (MRE) when compared with the LSM method. The proposed model achieves an MAE of 0.025 and an MRE of 1.32% in the testing dataset, while the LSM method has an MAE of 0.043 and an MRE of 2.56% in the same dataset. Therefore, the proposed non-parametric analysis model based on the BP neural network can achieve higher accuracy in meter coefficient analysis when compared with the traditional LSM method. This study provides a novel non-parametric analysis method with practical reference value for the electricity industry in energy metering and load forecasting.
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Affiliation(s)
- Yuqiang Yang
- State Grid Zhejiang Electric Power Co. Ltd, Hanzghou City, 310007, China
| | - Ruoyun Hu
- Department of Marketing, State Grid Zhejiang Electric Power Co. Ltd, Hanzghou City, 310007, China
| | - Weifeng Wang
- Department of Marketing, State Grid Zhejiang Electric Power Co. Ltd, Hanzghou City, 310007, China
| | - Tuomu Zhang
- Beijing Zhixiang Technology Co., Ltd., Beijing City, 100000, China.
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2
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Li N, Zhang G, Zhang X, Liu Y, Kong Y, Wang M, Ren X. A rapid-floating natural polysaccharide gel-raft with double-effect for the treatment of gastroesophageal reflux disease. Int J Biol Macromol 2024; 261:129667. [PMID: 38272401 DOI: 10.1016/j.ijbiomac.2024.129667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 01/14/2024] [Accepted: 01/20/2024] [Indexed: 01/27/2024]
Abstract
Gastroesophageal reflux disease (GERD) is a prevalent gastrointestinal condition characterized by regurgitating stomach contents into the esophagus, causing mucosal damage or erosion. Clinical physical protection treatment mainly relies on the use of floating rafts. Bletilla striata (BS) is widely regarded as the first-choice drug for treating digestive tract injuries in Chinese Medicine. The rapid-floating gel-raft (B-R) was prepared via a one-step swelling method using natural BS polysaccharide and glyceryl monooleate. Panax notoginseng saponins (PNS) were loaded to further prepare P/B-R according to clinical experience. Possessing hydrophobic dense, stratified porous structure and stable rheological properties, an outperforming floating performance of P/B-R was proven compared with Gaviscon® (alginate-antacid formulation) in vitro. In vivo imaging results showed that P/B-R can retain and adhere to the gastric mucosa of rats for up to 90 min, protecting and repairing the mucosa. Besides physical protection in situ, the systemic effects of antioxidant and anti-inflammatory actions for treating GERD were achieved through the intestinal release of PNS. Acid-labile PNS was protected by P/B-R against gastric acid, attaining the desired release and permeability. A significantly effective mucosa injury protective effect of P/B-R was found in ethanol-induced gastric damage model on rats. Moreover, P/B-R exhibits excellent biosafety at the cellular level.
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Affiliation(s)
- Na Li
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China; State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Guoqin Zhang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Xueyan Zhang
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Yi Liu
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China
| | - Yan Kong
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China
| | - Meng Wang
- State Key Laboratory of Component-based Chinese Medicine, Tianjin University of Traditional Chinese Medicine, Tianjin 301617, China; Haihe Laboratory of Modern Chinese Medicine, Tianjin 301617, PR China..
| | - Xiaoliang Ren
- School of Chinese Materia Medica, Tianjin University of Traditional Chinese Medicine, Tianjin 300193, China.
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3
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Yarahmadi A, Afkhami H. The role of microbiomes in gastrointestinal cancers: new insights. Front Oncol 2024; 13:1344328. [PMID: 38361500 PMCID: PMC10867565 DOI: 10.3389/fonc.2023.1344328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 12/20/2023] [Indexed: 02/17/2024] Open
Abstract
Gastrointestinal (GI) cancers constitute more than 33% of new cancer cases worldwide and pose a considerable burden on public health. There exists a growing body of evidence that has systematically recorded an upward trajectory in GI malignancies within the last 5 to 10 years, thus presenting a formidable menace to the health of the human population. The perturbations in GI microbiota may have a noteworthy influence on the advancement of GI cancers; however, the precise mechanisms behind this association are still not comprehensively understood. Some bacteria have been observed to support cancer development, while others seem to provide a safeguard against it. Recent studies have indicated that alterations in the composition and abundance of microbiomes could be associated with the progression of various GI cancers, such as colorectal, gastric, hepatic, and esophageal cancers. Within this comprehensive analysis, we examine the significance of microbiomes, particularly those located in the intestines, in GI cancers. Furthermore, we explore the impact of microbiomes on various treatment modalities for GI cancer, including chemotherapy, immunotherapy, and radiotherapy. Additionally, we delve into the intricate mechanisms through which intestinal microbes influence the efficacy of GI cancer treatments.
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Affiliation(s)
- Aref Yarahmadi
- Department of Biology, Khorramabad Branch, Islamic Azad University, Khorramabad, Iran
| | - Hamed Afkhami
- Nervous System Stem Cells Research Center, Semnan University of Medical Sciences, Semnan, Iran
- Cellular and Molecular Research Center, Qom University of Medical Sciences, Qom, Iran
- Department of Medical Microbiology, Faculty of Medicine, Shahed University, Tehran, Iran
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4
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Chen J, Zhu J, Lu W, Wang H, Pan M, Tian P, Zhao J, Zhang H, Chen W. Uncovering Predictive Factors and Interventions for Restoring Microecological Diversity after Antibiotic Disturbance. Nutrients 2023; 15:3925. [PMID: 37764709 PMCID: PMC10536327 DOI: 10.3390/nu15183925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/04/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
Antibiotic treatment can lead to a loss of diversity of gut microbiota and may adversely affect gut microbiota composition and host health. Previous studies have indicated that the recovery of gut microbes from antibiotic-induced disruption may be guided by specific microbial species. We expect to predict recovery or non-recovery using these crucial species or other indices after antibiotic treatment only when the gut microbiota changes. This study focused on this prediction problem using a novel ensemble learning framework to identify a set of common and reasonably predictive recovery-associated bacterial species (p-RABs), enabling us to predict the host microbiome recovery status under broad-spectrum antibiotic treatment. Our findings also propose other predictive indicators, suggesting that higher taxonomic and functional diversity may correlate with an increased likelihood of successful recovery. Furthermore, to explore the validity of p-RABs, we performed a metabolic support analysis and identified Akkermansia muciniphila and Bacteroides uniformis as potential key supporting species for reconstruction interventions. Experimental results from a C57BL/6J male mouse model demonstrated the effectiveness of p-RABs in facilitating intestinal microbial reconstitution. Thus, we proved the reliability of the new p-RABs and validated a practical intervention scheme for gut microbiota reconstruction under antibiotic disturbance.
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Affiliation(s)
- Jing Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jinlin Zhu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Wenwei Lu
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- International Joint Research Laboratory for Pharmabiotics & Antibiotic Resistance, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hongchao Wang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Mingluo Pan
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Peijun Tian
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
| | - Jianxin Zhao
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
| | - Hao Zhang
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- (Yangzhou) Institute of Food Biotechnology, Jiangnan University, Yangzhou 225004, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
- Wuxi Translational Medicine Research Center and Jiangsu Translational Medicine Research Institute Wuxi Branch, Wuxi 214122, China
| | - Wei Chen
- State Key Laboratory of Food Science and Resources, Jiangnan University, Wuxi 214122, China; (J.C.); (W.L.); (H.W.); (M.P.); (P.T.); (J.Z.); (H.Z.); (W.C.)
- School of Food Science and Technology, Jiangnan University, Wuxi 214122, China
- National Engineering Research Center for Functional Food, Jiangnan University, Wuxi 214122, China
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5
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Karpe AV, Beale DJ, Tran CD. Intelligent Biological Networks: Improving Anti-Microbial Resistance Resilience through Nutritional Interventions to Understand Protozoal Gut Infections. Microorganisms 2023; 11:1800. [PMID: 37512972 PMCID: PMC10383877 DOI: 10.3390/microorganisms11071800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 07/10/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Enteric protozoan pathogenic infections significantly contribute to the global burden of gastrointestinal illnesses. Their occurrence is considerable within remote and indigenous communities and regions due to reduced access to clean water and adequate sanitation. The robustness of these pathogens leads to a requirement of harsh treatment methods, such as medicinal drugs or antibiotics. However, in addition to protozoal infection itself, these treatments impact the gut microbiome and create dysbiosis. This often leads to opportunistic pathogen invasion, anti-microbial resistance, or functional gastrointestinal disorders, such as irritable bowel syndrome. Moreover, these impacts do not remain confined to the gut and are reflected across the gut-brain, gut-liver, and gut-lung axes, among others. Therefore, apart from medicinal treatment, nutritional supplementation is also a key aspect of providing recovery from this dysbiosis. Future proteins, prebiotics, probiotics, synbiotics, and food formulations offer a good solution to remedy this dysbiosis. Furthermore, nutritional supplementation also helps to build resilience against opportunistic pathogens and potential future infections and disorders that may arise due to the dysbiosis. Systems biology techniques have shown to be highly effective tools to understand the biochemistry of these processes. Systems biology techniques characterize the fundamental host-pathogen interaction biochemical pathways at various infection and recovery stages. This same mechanism also allows the impact of the abovementioned treatment methods of gut microbiome remediation to be tracked. This manuscript discusses system biology approaches, analytical techniques, and interaction and association networks, to understand (1) infection mechanisms and current global status; (2) cross-organ impacts of dysbiosis, particularly within the gut-liver and gut-lung axes; and (3) nutritional interventions. This study highlights the impact of anti-microbial resistance and multi-drug resistance from the perspective of protozoal infections. It also highlights the role of nutritional interventions to add resilience against the chronic problems caused by these phenomena.
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Affiliation(s)
- Avinash V Karpe
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Black Mountain Science and Innovation Park, Acton, ACT 2601, Australia
- Socio-Eternal Thinking for Unity (SETU), Melbourne, VIC 3805, Australia
| | - David J Beale
- Environment, Commonwealth Scientific and Industrial Research Organisation, Ecosciences Precinct, Dutton Park, QLD 4102, Australia
| | - Cuong D Tran
- Health and Biosecurity, Commonwealth Scientific and Industrial Research Organisation, Gate 13 Kintore Ave., Adelaide, SA 5000, Australia
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6
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Weerasuriya W, Saunders JE, Kis L, Ho TT, Xu K, Lemas DJ, Groer MW, Louis-Jacques AF. Maternal Gut Microbiota in the Postpartum Period: A Systematic Review. Eur J Obstet Gynecol Reprod Biol 2023; 285:130-147. [PMID: 37116306 DOI: 10.1016/j.ejogrb.2023.03.042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/26/2023] [Accepted: 03/31/2023] [Indexed: 04/03/2023]
Abstract
Studies have demonstrated the importance of the gut microbiota during pregnancy, and there is emerging literature on the postpartum maternal gut microbiota. The primary objective of this paper was to synthesize the literature on the postpartum gut microbiome composition and diversity measured in stool samples from healthy mothers of predominantly term infants. The secondary objectives were (1) to identify biological and environmental factors that influence postpartum maternal gut microbiota and (2) to assess health conditions and clinical intermediate measures associated with postpartum gut microbiota changes in all mothers. Electronic searches were conducted November 9, 2020 and updated July 25, 2021 without publication time limits on PubMed, Embase, CINHAL, Scopus, Cochrane Library, BioArchives, and OpenGrey.eu. Primary research on maternal gut microbiota in the postpartum (up to one year after childbirth) were eligible. Postpartum gut microbiota comparisons to pregnancy or non-pregnancy gut microbiota were of interest, therefore, studies examining these in addition to the postpartum were included. Studies were excluded if they were only conducted in animals, infants, pregnancy, or microbiome of other body locations (e.g., vaginal). Data extraction of microbial composition and diversity were completed and synthesized narratively. Studies were assessed for risk of bias. A total of 2512 articles were screened after deduplication and 27 were included in this review. Of the 27 included studies, 22 addressed the primary objective. Firmicutes was the predominant phylum in the early (<6 weeks) and late postpartum (6 weeks to 1 year). In early postpartum, Bacteroides was the predominant genus. Findings from longitudinal assessments of alpha and beta diversity from the early to the late postpartum varied. Nineteen of the 27 studies assessed biological and environmental factors influencing the postpartum gut microbial profile changes. Timing of delivery, probiotic supplementation, triclosan exposure, and certain diets influenced the postpartum gut microbiota. Regarding health conditions and intermediate clinical measures assessed in 8 studies; inflammatory bowel disease, postpartum depression, early-onset preeclampsia, gestational diabetes, excessive gestational weight gain, and anthropometric measures such as body mass index and waist-to-hip ratio were related to gut microbiota changes. There is limited data on the maternal postpartum gut microbiota and how it influences maternal health. We need to understand the postpartum maternal gut microbiome, establish how it differs from non-pregnancy and pregnancy states, and determine biological and environmental influencers. Future research of the gut microbiome's significance for the birthing parent in the postpartum could lead to a new understanding of how to improve maternal short and long-term health.
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7
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Geometrical congruence, greedy navigability and myopic transfer in complex networks and brain connectomes. Nat Commun 2022; 13:7308. [PMID: 36437254 PMCID: PMC9701786 DOI: 10.1038/s41467-022-34634-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/01/2022] [Indexed: 11/28/2022] Open
Abstract
We introduce in network geometry a measure of geometrical congruence (GC) to evaluate the extent a network topology follows an underlying geometry. This requires finding all topological shortest-paths for each nonadjacent node pair in the network: a nontrivial computational task. Hence, we propose an optimized algorithm that reduces 26 years of worst scenario computation to one week parallel computing. Analysing artificial networks with patent geometry we discover that, different from current belief, hyperbolic networks do not show in general high GC and efficient greedy navigability (GN) with respect to the geodesics. The myopic transfer which rules GN works best only when degree-distribution power-law exponent is strictly close to two. Analysing real networks-whose geometry is often latent-GC overcomes GN as marker to differentiate phenotypical states in macroscale structural-MRI brain connectomes, suggesting connectomes might have a latent neurobiological geometry accounting for more information than the visible tridimensional Euclidean.
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8
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Beyond Basic Diversity Estimates-Analytical Tools for Mechanistic Interpretations of Amplicon Sequencing Data. Microorganisms 2022; 10:microorganisms10101961. [PMID: 36296237 PMCID: PMC9609705 DOI: 10.3390/microorganisms10101961] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/29/2022] [Accepted: 09/30/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding microbial ecology through amplifying short read regions, typically 16S rRNA for prokaryotic species or 18S rRNA for eukaryotic species, remains a popular, economical choice. These methods provide relative abundances of key microbial taxa, which, depending on the experimental design, can be used to infer mechanistic ecological underpinnings. In this review, we discuss recent advancements in in situ analytical tools that have the power to elucidate ecological phenomena, unveil the metabolic potential of microbial communities, identify complex multidimensional interactions between species, and compare stability and complexity under different conditions. Additionally, we highlight methods that incorporate various modalities and additional information, which in combination with abundance data, can help us understand how microbial communities respond to change in a typical ecosystem. Whilst the field of microbial informatics continues to progress substantially, our emphasis is on popular methods that are applicable to a broad range of study designs. The application of these methods can increase our mechanistic understanding of the ongoing dynamics of complex microbial communities.
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9
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Windels SFL, Malod-Dognin N, Pržulj N. Identifying cellular cancer mechanisms through pathway-driven data integration. Bioinformatics 2022; 38:4344-4351. [PMID: 35916710 PMCID: PMC9477533 DOI: 10.1093/bioinformatics/btac493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 06/14/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Cancer is a genetic disease in which accumulated mutations of driver genes induce a functional reorganization of the cell by reprogramming cellular pathways. Current approaches identify cancer pathways as those most internally perturbed by gene expression changes. However, driver genes characteristically perform hub roles between pathways. Therefore, we hypothesize that cancer pathways should be identified by changes in their pathway-pathway relationships. RESULTS To learn an embedding space that captures the relationships between pathways in a healthy cell, we propose pathway-driven non-negative matrix tri-factorization. In this space, we determine condition-specific (i.e. diseased and healthy) embeddings of pathways and genes. Based on these embeddings, we define our 'NMTF centrality' to measure a pathway's or gene's functional importance, and our 'moving distance', to measure the change in its functional relationships. We combine both measures to predict 15 genes and pathways involved in four major cancers, predicting 60 gene-cancer associations in total, covering 28 unique genes. To further exploit driver genes' tendency to perform hub roles, we model our network data using graphlet adjacency, which considers nodes adjacent if their interaction patterns form specific shapes (e.g. paths or triangles). We find that the predicted genes rewire pathway-pathway interactions in the immune system and provide literary evidence that many are druggable (15/28) and implicated in the associated cancers (47/60). We predict six druggable cancer-specific drug targets. AVAILABILITY AND IMPLEMENTATION The code and data are available at: https://gitlab.bsc.es/swindels/pathway_driven_nmtf. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Sam F L Windels
- Department of Computer Science, University College London, London WC1E 6BT, UK,Barcelona Supercomputing Center, 08034 Barcelona, Spain
| | - Noël Malod-Dognin
- Department of Computer Science, University College London, London WC1E 6BT, UK,Barcelona Supercomputing Center, 08034 Barcelona, Spain
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10
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Schwarz C, Mathieu J, Laverde Gomez JA, Yu P, Alvarez PJJ. Renaissance for Phage-Based Bacterial Control. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022; 56:4691-4701. [PMID: 34793127 DOI: 10.1021/acs.est.1c06232] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Bacteriophages (phages) are an underutilized biological resource with vast potential for pathogen control and microbiome editing. Phage research and commercialization have increased rapidly in biomedical and agricultural industries, but adoption has been limited elsewhere. Nevertheless, converging advances in DNA sequencing, bioinformatics, microbial ecology, and synthetic biology are now poised to broaden phage applications beyond pathogen control toward the manipulation of microbial communities for defined functional improvements. Enhancements in sequencing combined with network analysis make it now feasible to identify and disrupt microbial associations to elicit desirable shifts in community structure or function, indirectly modulate species abundance, and target hub or keystone species to achieve broad functional shifts. Sequencing and bioinformatic advancements are also facilitating the use of temperate phages for safe gene delivery applications. Finally, integration of synthetic biology stands to create novel phage chassis and modular genetic components. While some fundamental, regulatory, and commercialization barriers to widespread phage use remain, many major challenges that have impeded the field now have workable solutions. Thus, a new dawn for phage-based (chemical-free) precise biocontrol and microbiome editing is on the horizon to enhance, suppress, or modulate microbial activities important for public health, food security, and more sustainable energy production and water reuse.
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Affiliation(s)
- Cory Schwarz
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jacques Mathieu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Jenny A Laverde Gomez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
| | - Pingfeng Yu
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
| | - Pedro J J Alvarez
- Department of Civil and Environmental Engineering, Rice University, Houston, Texas 77005, United States
- Sentinel Environmental, Houston, Texas 77082, United States
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11
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Moran MA, Kujawinski EB, Schroer WF, Amin SA, Bates NR, Bertrand EM, Braakman R, Brown CT, Covert MW, Doney SC, Dyhrman ST, Edison AS, Eren AM, Levine NM, Li L, Ross AC, Saito MA, Santoro AE, Segrè D, Shade A, Sullivan MB, Vardi A. Microbial metabolites in the marine carbon cycle. Nat Microbiol 2022; 7:508-523. [PMID: 35365785 DOI: 10.1038/s41564-022-01090-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/23/2022] [Indexed: 01/08/2023]
Abstract
One-quarter of photosynthesis-derived carbon on Earth rapidly cycles through a set of short-lived seawater metabolites that are generated from the activities of marine phytoplankton, bacteria, grazers and viruses. Here we discuss the sources of microbial metabolites in the surface ocean, their roles in ecology and biogeochemistry, and approaches that can be used to analyse them from chemistry, biology, modelling and data science. Although microbial-derived metabolites account for only a minor fraction of the total reservoir of marine dissolved organic carbon, their flux and fate underpins the central role of the ocean in sustaining life on Earth.
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Affiliation(s)
- Mary Ann Moran
- Department of Marine Sciences, University of Georgia, Athens, GA, USA.
| | - Elizabeth B Kujawinski
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA, USA.
| | - William F Schroer
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Shady A Amin
- Division of Science, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Nicholas R Bates
- Bermuda Institute of Ocean Sciences, St George's, Bermuda.,School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Rogier Braakman
- Departments of Earth, Atmospheric and Planetary Sciences, and Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - C Titus Brown
- Population Health and Reproduction, School of Veterinary Medicine, University of California, Davis, Davis, CA, USA
| | - Markus W Covert
- Department of Bioengineering, Stanford University, Stanford, CA, USA
| | - Scott C Doney
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA, USA
| | - Sonya T Dyhrman
- Lamont-Doherty Earth Observatory, Columbia University, Palisades, NY, USA.,Department of Earth and Environmental Science, Columbia University, Palisades, NY, USA
| | - Arthur S Edison
- Departments of Biochemistry and Genetics, Complex Carbohydrate Research Center, University of Georgia, Athens, GA, USA
| | - A Murat Eren
- Josephine Bay Paul Center, Marine Biological Laboratory, Woods Hole, MA, USA.,Helmholtz-Institute for Functional Marine Biodiversity (HIFMB), University of Oldenburg, Oldenburg, Germany
| | - Naomi M Levine
- Marine and Environmental Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Avena C Ross
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Mak A Saito
- Department of Marine Sciences, University of Georgia, Athens, GA, USA
| | - Alyson E Santoro
- Department of Ecology, Evolution and Marine Biology, University of California, Santa Barbara, CA, USA
| | - Daniel Segrè
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Ashley Shade
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, USA
| | - Matthew B Sullivan
- Departments of Microbiology and Civil, Environmental, and Geodetic Engineering, and Center of Microbiome Science, The Ohio State University, Columbus, OH, USA
| | - Assaf Vardi
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
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Vemuri R, Martoni CJ, Kavanagh K, Eri R. Lactobacillus acidophilus DDS-1 Modulates the Gut Microbial Co-Occurrence Networks in Aging Mice. Nutrients 2022; 14:nu14050977. [PMID: 35267950 PMCID: PMC8912519 DOI: 10.3390/nu14050977] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 02/18/2022] [Accepted: 02/23/2022] [Indexed: 12/13/2022] Open
Abstract
Age-related alterations in the gut microbiome composition and its impacts on the host’s health have been well-described; however, detailed analyses of the gut microbial structure defining ecological microbe–microbe interactions are limited. One of the ways to determine these interactions is by understanding microbial co-occurrence patterns. We previously showed promising abilities of Lactobacillus acidophilus DDS-1 on the aging gut microbiome and immune system. However, the potential of the DDS-1 strain to modulate microbial co-occurrence patterns is unknown. Hence, we aimed to investigate the ability of L. acidophilus DDS-1 to modulate the fecal-, mucosal-, and cecal-related microbial co-occurrence networks in young and aging C57BL/6J mice. Our Kendall’s tau correlation measures of co-occurrence revealed age-related changes in the gut microbiome, which were characterized by a reduced number of nodes and associations across sample types when compared to younger mice. After four-week supplementation, L. acidophilus DDS-1 differentially modulated the overall microbial community structure in fecal and mucosal samples as compared to cecal samples. Beneficial bacteria such as Lactobacillus, Oscillospira, and Akkermansia acted as connectors in aging networks in response to L. acidophilus DDS-1 supplementation. Our findings provided the first evidence of the DDS-1-induced gut microbial ecological interactions, revealing the complex structure of microbial ecosystems with age.
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Affiliation(s)
- Ravichandra Vemuri
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA;
- College of Health and Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
- Correspondence:
| | | | - Kylie Kavanagh
- Department of Pathology, Section on Comparative Medicine, Wake Forest School of Medicine, Medical Center Boulevard, Winston-Salem, NC 27157, USA;
- Department of Biomedicine, University of Tasmania, Hobart, TAS 7000, Australia
| | - Rajaraman Eri
- College of Health and Medicine, School of Health Sciences, University of Tasmania, Launceston, TAS 7248, Australia;
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Medial prefrontal and occipito-temporal activity at encoding determines enhanced recognition of threatening faces after 1.5 years. Brain Struct Funct 2022; 227:1655-1672. [PMID: 35174416 DOI: 10.1007/s00429-022-02462-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 01/24/2022] [Indexed: 11/02/2022]
Abstract
Studies demonstrated that faces with threatening emotional expressions are better remembered than non-threatening faces. However, whether this memory advantage persists over years and which neural systems underlie such an effect remains unknown. Here, we employed an individual difference approach to examine whether the neural activity during incidental encoding was associated with differential recognition of faces with emotional expressions (angry, fearful, happy, sad and neutral) after a retention interval of > 1.5 years (N = 89). Behaviorally, we found a better recognition for threatening (angry, fearful) versus non-threatening (happy and neutral) faces after a delay of > 1.5 years, which was driven by forgetting of non-threatening faces compared with immediate recognition after encoding. Multivariate principal component analysis (PCA) on the behavioral responses further confirmed the discriminative recognition performance between threatening and non-threatening faces. A voxel-wise whole-brain analysis on the concomitantly acquired functional magnetic resonance imaging (fMRI) data during incidental encoding revealed that neural activity in bilateral inferior occipital gyrus (IOG) and ventromedial prefrontal/orbitofrontal cortex (vmPFC/OFC) was associated with the individual differences in the discriminative emotional face recognition performance measured by an innovative behavioral pattern similarity analysis (BPSA). The left fusiform face area (FFA) was additionally determined using a regionally focused analysis. Overall, the present study provides evidence that threatening facial expressions lead to persistent face recognition over periods of > 1.5 years, and that differential encoding-related activity in the medial prefrontal cortex and occipito-temporal cortex may underlie this effect.
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Fujimori S. Progress in elucidating the relationship between Helicobacter pylori infection and intestinal diseases. World J Gastroenterol 2021; 27:8040-8046. [PMID: 35068852 PMCID: PMC8704277 DOI: 10.3748/wjg.v27.i47.8040] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 06/30/2021] [Accepted: 12/08/2021] [Indexed: 02/06/2023] Open
Abstract
Helicobacter pylori (H. pylori) infection causes changes to the intestinal flora, such as small intestinal bacterial overgrowth, and increases gastric acid secretion-stimulating gastrointestinal hormones, mainly gastrin, due to a decrease in gastric acid caused by atrophic gastritis. In addition, the cellular components of H. pylori travel through the intestinal tract, so the bacterial infection affects the immune system. Therefore, the effects of H. pylori infection are observed not only in the stomach and the proximal duodenum but also in the small and large intestines. In particular, meta-analyses reported that H. pylori-infected individuals had an increased risk of colorectal adenoma and colorectal cancer. Moreover, a recent study reported that the risk of developing colorectal cancer was increased in subjects carrying H. pylori vacuolating cytotoxin A antibody. In addition, it has been reported that H. pylori infection exacerbates the symptoms of Fabry’s disease and familial Mediterranean fever attack and is involved in irritable bowel syndrome and small intestinal ulcers. On the other hand, some studies have reported that the frequency of ulcerative colitis, Crohn’s disease, and celiac disease is low in H. pylori-infected individuals. Thus, H. pylori infection is considered to have various effects on the small and large intestines. However, few studies have reported on these issues, and the details of their effects have not been well elucidated. Therefore, additional studies are needed.
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Affiliation(s)
- Shunji Fujimori
- Department of Gastroenterology, Chiba Hokusoh Hospital, Nippon Medical School, Chiba 270-1694, Japan
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Cannistraci CV, Valsecchi MG, Capua I. Age-sex population adjusted analysis of disease severity in epidemics as a tool to devise public health policies for COVID-19. Sci Rep 2021; 11:11787. [PMID: 34083555 PMCID: PMC8175671 DOI: 10.1038/s41598-021-89615-4] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 04/28/2021] [Indexed: 11/08/2022] Open
Abstract
Governments continue to update social intervention strategies to contain COVID-19 infections. However, investigation of COVID-19 severity indicators across the population might help to design more precise strategies, balancing the need to keep people safe and to reduce the socio-economic burden of generalized restriction precedures. Here, we propose a method for age-sex population-adjusted analysis of disease severity in epidemics that has the advantage to use simple and repeatable variables, which are daily or weekly available. This allows to monitor the effect of public health policies in short term, and to repeat these calculations over time to surveille epidemic dynamics and impact. Our method can help to define a risk-categorization of likeliness to develop a severe COVID-19 disease which requires intensive care or is indicative of a higher risk of dying. Indeed, analysis of suitable open-access COVID-19 data in three European countries indicates that individuals in the 0-40 age interval and females under 60 are significantly less likely to develop a severe condition and die, whereas males equal or above 60 are more likely at risk of severe disease and death. Hence, a combination of age-adaptive and sex-balanced guidelines for social interventions could represent key public health management tools for policymakers.
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Affiliation(s)
- Carlo Vittorio Cannistraci
- Center for Complex Network Intelligence (CCNI) at the Tsinghua Laboratory of Brain and Intelligence (THBI), Department of Biomedical Engineering, Tsinghua University, 160 Chengfu Rd., SanCaiTang Building, Haidian District, Beijing, 100084, China.
- Biomedical Cybernetics Group, Biotechnology Center (BIOTEC), Center for Molecular and Cellular Bioengineering (CMCB), Center for Systems Biology Dresden (CSBD), Department of Physics, Technische Universität Dresden, Tatzberg 47/49, 01307, Dresden, Germany.
| | - Maria Grazia Valsecchi
- Bicocca Center of Bioinformatics, Biostatistics and Bioimaging, School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy
| | - Ilaria Capua
- One Health Center of Excellence, University of Florida, Gainesville, FL, USA.
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