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Wang J, Peipoch M, Guo X, Kan J. Convergence of biofilm successional trajectories initiated during contrasting seasons. Front Microbiol 2022; 13:991816. [PMID: 36187986 PMCID: PMC9522907 DOI: 10.3389/fmicb.2022.991816] [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: 07/12/2022] [Accepted: 08/26/2022] [Indexed: 12/02/2022] Open
Abstract
Biofilm communities play a major role in explaining the temporal variation of biogeochemical conditions in freshwater ecosystems, and yet we know little about how these complex microbial communities change over time (aka succession), and from different initial conditions, in comparison to other stream communities. This has resulted in limited knowledge on how biofilm community structure and microbial colonization vary over relevant time scales to become mature biofilms capable of significant alteration of the freshwater environment in which they live. Here, we monitored successional trajectories of biofilm communities from summer and winter in a headwater stream and evaluated their structural state over time by DNA high-throughput sequencing. Significant differences in biofilm composition were observed when microbial colonization started in the summer vs. winter seasons, with higher percentage of algae (Bacillariophyta) and Bacteroidetes in winter-initiated samples but higher abundance of Proteobacteria (e.g., Rhizobiales, Rhodobacterales, Sphingomonadales, and Burkholderiales), Actinobacteria, and Chloroflexi in summer-initiated samples. Interestingly, results showed that despite seasonal effects on early biofilm succession, biofilm community structures converged after 70 days, suggesting the existence of a stable, mature community in the stream that is independent of the environmental conditions during biofilm colonization. Overall, our results show that algae are important in the early development of biofilm communities during winter, while heterotrophic bacteria play a more critical role during summer colonization and development of biofilms.
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Affiliation(s)
- Jing Wang
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
- Stroud Water Research Center, Avondale, PA, United States
| | - Marc Peipoch
- Stroud Water Research Center, Avondale, PA, United States
| | - Xiaoxiao Guo
- Tianjin Key Laboratory of Animal and Plant Resistance, Tianjin Key Laboratory of Conservation and Utilization of Animal Diversity, Tianjin Normal University, Tianjin, China
| | - Jinjun Kan
- Stroud Water Research Center, Avondale, PA, United States
- *Correspondence: Jinjun Kan,
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Lang JM, Sedgeman LR, Cai L, Layne JD, Wang Z, Pan C, Lee R, Temel RE, Lusis AJ. Dietary and Pharmacologic Manipulations of Host Lipids and Their Interaction With the Gut Microbiome in Non-human Primates. Front Med (Lausanne) 2021; 8:646710. [PMID: 34513856 PMCID: PMC8426918 DOI: 10.3389/fmed.2021.646710] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 08/03/2021] [Indexed: 12/12/2022] Open
Abstract
The gut microbiome influences nutrient processing as well as host physiology. Plasma lipid levels have been associated with the microbiome, although the underlying mechanisms are largely unknown, and the effects of dietary lipids on the gut microbiome in humans are not well-studied. We used a compilation of four studies utilizing non-human primates (Chlorocebus aethiops and Macaca fascicularis) with treatments that manipulated plasma lipid levels using dietary and pharmacological techniques, and characterized the microbiome using 16S rDNA. High-fat diets significantly reduced alpha diversity (Shannon) and the Firmicutes/Bacteroidetes ratio compared to chow diets, even when the diets had different compositions and were applied in different orders. When analyzed for differential abundance using DESeq2, Bulleidia, Clostridium, Ruminococcus, Eubacterium, Coprocacillus, Lachnospira, Blautia, Coprococcus, and Oscillospira were greater in both chow diets while Succinivibrio, Collinsella, Streptococcus, and Lactococcus were greater in both high-fat diets (oleic blend or lard fat source). Dietary cholesterol levels did not affect the microbiome and neither did alterations of plasma lipid levels through treatments of miR-33 antisense oligonucleotide (anti-miR-33), Niemann-Pick C1-Like 1 (NPC1L1) antisense oligonucleotide (ASO), and inducible degrader of LDLR (IDOL) ASO. However, a liver X receptor (LXR) agonist shifted the microbiome and decreased bile acid levels. Fifteen genera increased with the LXR agonist, while seven genera decreased. Pseudomonas increased on the LXR agonist and was negatively correlated to deoxycholic acid, cholic acid, and total bile acids while Ruminococcus was positively correlated with taurolithocholic acid and taurodeoxycholic acid. Seven of the nine bile acids identified in the feces significantly decreased due to the LXR agonist, and total bile acids (nmol/g) was reduced by 62%. These results indicate that plasma lipid levels have, at most, a modest effect on the microbiome, whereas bile acids, derived in part from plasma lipids, are likely responsible for the indirect relationship between lipid levels and the microbiome.
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Affiliation(s)
- Jennifer M. Lang
- Departments of Medicine, Microbiology and Human Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Leslie R. Sedgeman
- Department of Medicine, Division of Cardiology, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lei Cai
- Cardiovascular Research Center, University of Kentucky, Lexington, KY, United States
| | - Joseph D. Layne
- Cardiovascular Research Center, University of Kentucky, Lexington, KY, United States
- Cardiovascular and Metabolic Diseases, Novartis Institutes for Biomedical Research, Cambridge, MA, United States
| | - Zhen Wang
- Department of Physiology, School of Basic Medical Sciences, Shandong University, Jinan, China
| | - Calvin Pan
- Departments of Medicine, Microbiology and Human Genetics, University of California, Los Angeles, Los Angeles, CA, United States
| | - Richard Lee
- Ionis Pharmaceuticals, Carlsbad, CA, United States
| | - Ryan E. Temel
- Cardiovascular and Metabolic Diseases, Novartis Institutes for Biomedical Research, Cambridge, MA, United States
- Department of Physiology, University of Kentucky, Lexington, KY, United States
| | - Aldons J. Lusis
- Departments of Medicine, Microbiology and Human Genetics, University of California, Los Angeles, Los Angeles, CA, United States
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Larson CE, Pechal JL, Gerig BS, Chaloner DT, Lamberti GA, Benbow ME. Microbial Community Response to a Novel Salmon Resource Subsidy. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2019.00505] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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Cuellar-Gempeler C, Munguia P. Habitat filters mediate successional trajectories in bacterial communities associated with the striped shore crab. Oecologia 2019; 191:957-970. [PMID: 31690999 DOI: 10.1007/s00442-019-04549-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 10/28/2019] [Indexed: 02/01/2023]
Abstract
The relative importance of stochastic- and niche-based processes shifts during successional time and across different types of habitats. Microbial biofilms are known to undergo such successional shifts. However, little is known about the interaction between these successional trajectories and habitat filters. Harsh habitat filters could affect biofilm successional trajectories by strengthening niche-based processes and weakening stochastic processes. We used mesocosms to track successional trajectories in bacterial communities associated with the striped shore crab (Pachygrapsus transversus). We followed replicated microbial communities under strong and weak habitat filters associated with the crab's gut and carapace. For bacteria, colonization of the crab's gut is constrained by strong chemical and physical filtering, while the carapace remains relatively open for colonization. Consistent with successional models of bacterial biofilms, carapace microbial communities initially converged in community composition at day 8 and diverged thereafter. We expected gut microbial communities to deviate from the trajectory in the carapace and converge towards a subset of tolerant species. Instead, bacterial communities in the gut exhibited low richness, unchanging similarity in composition and turnover in species identities throughout the duration of our study. These habitat filter effects were linked with weak species interactions and low influence from colonization in the gut. If these findings are representative of differences in filter strength in a continuum of successional trajectories, habitat filters may provide basis for predictions that link successional models and habitat types.
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Affiliation(s)
| | - Pablo Munguia
- Royal Melbourne Institute of Technology, Melbourne, Australia
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He J, Guo J, Fu X, Cai J. Potential use of high-throughput sequencing of bacterial communities for postmortem submersion interval estimation. Braz J Microbiol 2019; 50:999-1010. [PMID: 31364013 DOI: 10.1007/s42770-019-00119-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Microorganisms play vital roles in the natural decomposition of carcasses in aquatic systems. Using high-throughput sequencing techniques, we evaluated the composition and succession of microbial communities throughout the decomposition of rat carcasses in freshwater. A total of 4,428,781 high-quality 16S rRNA gene sequences and 2144 operational taxonomic units were obtained. Further analysis revealed that the microbial composition differed significantly between the epinecrotic (rat skins) and the epilithic (rocks) samples. During the carcass decomposition process, Proteobacteria became the dominant phylum in the epinecrotic, epilithic, and environmental (water) samples, followed by Firmicutes in the epinecrotic samples and Bacteroidetes in the epilithic and water samples. Microbial communities were influenced by numerous environmental factors, such as dissolved oxygen content and conductivity. Our study provides new insight about postmortem submersion interval (PMSI) estimation in aquatic environments.
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Affiliation(s)
- Jing He
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Juanjuan Guo
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Xiaoliang Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China
| | - Jifeng Cai
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, Changsha, 410013, Hunan, People's Republic of China.
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Sukhanova EV, Shtykova YR, Suslova MY, Pestunova OS, Kostornova TY, Khanaev IV, Zimens EA, Podlesnaya GV, Parfenova VV. Diversity and Physiological and Biochemical Properties of Heterotrophic Bacteria Isolated from Lake Baikal Epilithic Biofilms. Microbiology (Reading) 2019. [DOI: 10.1134/s0026261719030147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Lang JM, Erb R, Pechal JL, Wallace JR, McEwan RW, Benbow ME. Microbial Biofilm Community Variation in Flowing Habitats: Potential Utility as Bioindicators of Postmortem Submersion Intervals. Microorganisms 2016; 4:microorganisms4010001. [PMID: 27681897 PMCID: PMC5029506 DOI: 10.3390/microorganisms4010001] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 12/08/2015] [Accepted: 12/14/2015] [Indexed: 01/01/2023] Open
Abstract
Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated ribosomal intergenic spacer analysis. Epinecrotic communities were significantly different from epilithic communities even though environmental factors associated with each stream location also had a significant influence on biofilm structure. All communities at both locations exhibited significant succession suggesting that changing communities throughout time is a general characteristic of stream biofilm communities. The implications resulting from this work are that epinecrotic communities have distinctive shifts at the first and second weeks, and therefore the potential to be used in forensic applications by associating successional changes with submersion time to estimate a PMSI. The influence of environmental factors, however, indicates the lack of a successional pattern with the same organisms and a focus on functional diversity may be more applicable in a forensic context.
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Affiliation(s)
- Jennifer M Lang
- Department of Biology, University of Dayton, Dayton, OH 45469-2320, USA.
| | - Racheal Erb
- Department of Biology, Millersville University, Millersville, PA 17551, USA.
| | - Jennifer L Pechal
- Department of Entomology, Michigan State University, 243 Natural Science Building, 288 Farm Lane, East Lansing, MI 48824, USA.
| | - John R Wallace
- Department of Biology, Millersville University, Millersville, PA 17551, USA.
| | - Ryan W McEwan
- Department of Biology, University of Dayton, Dayton, OH 45469-2320, USA.
| | - Mark Eric Benbow
- Department of Entomology, Michigan State University, 243 Natural Science Building, 288 Farm Lane, East Lansing, MI 48824, USA.
- Department of Osteopathic Medical Specialties, Michigan State University, 243 Natural Science Building, 288 Farm Lane, East Lansing, MI 48824, USA.
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