1
|
Jinato T, Anuntakarun S, Satthawiwat N, Chuaypen N, Tangkijvanich P. Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma. Appl Microbiol Biotechnol 2024; 108:34. [PMID: 38183473 PMCID: PMC10771587 DOI: 10.1007/s00253-023-12845-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 11/06/2023] [Accepted: 11/16/2023] [Indexed: 01/08/2024]
Abstract
Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis C-related HCC (NBNC-HCC). Fecal specimens were obtained from 16 healthy controls, 33 patients with viral-HCC (17 and 16 cases with hepatitis B virus (HBV) and hepatitis C virus (HCV) infection, respectively), and 18 patients with NBNC-HCC. Compositions of fecal microbiota were assessed by 16S rRNA sequencing. Bioinformatic analysis was performed by the DADA2 pipeline in the R program. Significantly different genera from the top 50 relative abundance were used to classify between subgroups of HCC by the Random Forest algorithm. Our data demonstrated that the HCC group had a significantly decreased alpha-diversity and changed microbial composition in comparison with healthy controls. Within the top 50 relative abundance, there were 11 genera including Faecalibacterium, Agathobacter, and Coprococcus that were significantly enhanced in Viral-HCC, while 5 genera such as Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium were enhanced in NBNC-HCC. Compared to Viral-HCC, the NBNC-HCC subgroup significantly reduced various short-chain fatty acid-producing bacteria, as well as declined fecal butyrate but elevated plasma surrogate markers of microbial translocation. Based on the machine learning algorithm, a high diagnostic accuracy to classify HCC subgroups was achieved with an area under the receiver-operating characteristic (ROC) curve (AUC) of 0.94. Collectively, these data revealed that gut dysbiosis was distinct according to etiological factors of HCC, which might play an essential role in hepatocarcinogenesis. These findings underscore the possible use of a gut microbiota signature for the diagnosis and therapeutic approaches regarding different subgroups of HCC. KEY POINTS: • Gut dysbiosis is connected to hepatocarcinogenesis and can be used as a novel biomarker. • Gut microbiota composition is significantly altered in different etiological factors of HCC. • Microbiota-based signature can accurately distinguish between Viral-HCC and NBNC-HCC.
Collapse
Affiliation(s)
- Thananya Jinato
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
- Doctor of Philosophy Program in Medical Sciences, Graduate Affairs, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Songtham Anuntakarun
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Nantawat Satthawiwat
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Natthaya Chuaypen
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| | - Pisit Tangkijvanich
- Center of Excellence in Hepatitis and Liver Cancer, Department of Biochemistry, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand.
| |
Collapse
|
2
|
Mykrä H, Aroviita J, Tolonen K, Turunen J, Weckström K, Weckström J, Hellsten S. Detecting mining impacts on freshwater ecosystems using replicated sampling before and after the impact. ENVIRONMENTAL MONITORING AND ASSESSMENT 2024; 196:635. [PMID: 38900337 PMCID: PMC11190011 DOI: 10.1007/s10661-024-12812-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/11/2024] [Indexed: 06/21/2024]
Abstract
Detecting human impact on freshwater ecosystems is problematic without rigorous assessment of temporal changes. Assessments of mining impacts are further complicated by the strong influence of local catchment geology on surface waters even in unmined environments. Such influence cannot be effectively considered by using broad-scale reference frameworks based on regionalization and stream types. Using the BACI (Before-After Control-Impact) design, we examined the impact of mining discharges on freshwater algae and macroinvertebrate communities resulting from the rerouting of treated wastewaters through a pipeline to larger water bodies in Northern and North-Eastern Finland. Impacted sites and control sites were sampled 1 to 2 years before and 1 to 3 years after the pipelines became operational. Stream diatom communities recovered from past loadings upstream of the pipeline (which was no longer impacted by wastewaters) after rerouting of the wastewaters, while no changes downstream from the pipeline were detected. Upstream from the pipeline, diatom species richness increased and changes in relative abundances of the most common diatom taxa as well as in the overall community composition were observed. The effects of the pipeline were less evident for stream macroinvertebrate communities. There was an indication that regional reference conditions used in national biomonitoring may not represent diatom communities in areas with a strong geochemical background influence. Lake profundal macroinvertebrate communities were impacted by past loadings before the construction of the pipeline, and the influence of the pipeline was observed only as changes in the abundances of a few individual species such as phantom midges (which increased in abundance in response to discharges directed through the pipeline). Our results highlight the variable influence of mining discharges on aquatic communities. Statistically strong monitoring programmes, such as BACI designs, are clearly needed to detect these influences.
Collapse
Affiliation(s)
- Heikki Mykrä
- Finnish Environment Institute, Nature Solutions, P.O. Box 413, 90014, Oulu, FI, Finland.
| | - Jukka Aroviita
- Finnish Environment Institute, Marine and Freshwater Solutions, P.O. Box 413, 90014, Oulu, FI, Finland
| | - Kimmo Tolonen
- Finnish Environment Institute, Nature Solutions, P.O. Box 413, 90014, Oulu, FI, Finland
| | - Jarno Turunen
- Finnish Environment Institute, Marine and Freshwater Solutions, P.O. Box 413, 90014, Oulu, FI, Finland
| | - Kaarina Weckström
- University of Helsinki, Ecosystems and Environment Research Programme, and Helsinki Institute of Sustainability Science (HELSUS), (Viikinkaari 1), P.O. Box 65, 00014, Helsinki, FI, Finland
| | - Jan Weckström
- University of Helsinki, Ecosystems and Environment Research Programme, and Helsinki Institute of Sustainability Science (HELSUS), (Viikinkaari 1), P.O. Box 65, 00014, Helsinki, FI, Finland
| | - Seppo Hellsten
- Finnish Environment Institute, Marine and Freshwater Solutions, P.O. Box 413, 90014, Oulu, FI, Finland
| |
Collapse
|
3
|
Dean CJ, Deng Y, Wehri TC, Pena-Mosca F, Ray T, Crooker BA, Godden SM, Caixeta LS, Noyes NR. The impact of kit, environment, and sampling contamination on the observed microbiome of bovine milk. mSystems 2024; 9:e0115823. [PMID: 38785438 DOI: 10.1128/msystems.01158-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 04/22/2024] [Indexed: 05/25/2024] Open
Abstract
In low-microbial biomass samples such as bovine milk, contaminants can outnumber endogenous bacteria. Because of this, milk microbiome research suffers from a critical knowledge gap, namely, does non-mastitis bovine milk contain a native microbiome? In this study, we sampled external and internal mammary epithelia and stripped and cisternal milk and used numerous negative controls, including air and sampling controls and extraction and library preparation blanks, to identify the potential sources of contamination. Two algorithms were used to mathematically remove contaminants and track the potential movement of microbes among samples. Results suggest that the majority (i.e., >75%) of sequence data generated from bovine milk and mammary epithelium samples represents contaminating DNA. Contaminants in milk samples were primarily sourced from DNA extraction kits and the internal and external skin of the teat, while teat canal and apex samples were mainly contaminated during the sampling process. After decontamination, the milk microbiome displayed a more dispersed, less diverse, and compositionally distinct bacterial profile compared with epithelial samples. Similar microbial compositions were observed between cisternal and stripped milk samples, as well as between teat apex and canal samples. Staphylococcus and Acinetobacter were the predominant genera detected in milk sample sequences, and bacterial culture showed growth of Staphylococcus and Corynebacterium spp. in 50% (7/14) of stripped milk samples and growth of Staphylococcus spp. in 7% (1/14) of cisternal milk samples. Our study suggests that microbiome data generated from milk samples obtained from clinically healthy bovine udders may be heavily biased by contaminants that enter the sample during sample collection and processing workflows.IMPORTANCEObtaining a non-contaminated sample of bovine milk is challenging due to the nature of the sampling environment and the route by which milk is typically extracted from the mammary gland. Furthermore, the very low bacterial biomass of bovine milk exacerbates the impacts of contaminant sequences in downstream analyses, which can lead to severe biases. Our finding showed that bovine milk contains very low bacterial biomass and each contamination event (including sampling procedure and DNA extraction process) introduces bacteria and/or DNA fragments that easily outnumber the native bacterial cells. This finding has important implications for our ability to draw robust conclusions from milk microbiome data, especially if the data have not been subjected to rigorous decontamination procedures. Based on these findings, we strongly urge researchers to include numerous negative controls into their sampling and sample processing workflows and to utilize several complementary methods for identifying potential contaminants within the resulting sequence data. These measures will improve the accuracy, reliability, reproducibility, and interpretability of milk microbiome data and research.
Collapse
Affiliation(s)
- C J Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - Y Deng
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T C Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - F Pena-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B A Crooker
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - S M Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L S Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N R Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
4
|
Yao H, Rinta-Kanto JM, Vassilev I, Kokko M. Methanol as a co-substrate with CO 2 enhances butyrate production in microbial electrosynthesis. Appl Microbiol Biotechnol 2024; 108:372. [PMID: 38874789 PMCID: PMC11178620 DOI: 10.1007/s00253-024-13218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 05/28/2024] [Accepted: 06/02/2024] [Indexed: 06/15/2024]
Abstract
Methanol is a promising feedstock for the bio-based economy as it can be derived from organic waste streams or produced electrochemically from CO2. Acetate production from CO2 in microbial electrosynthesis (MES) has been widely studied, while more valuable compounds such as butyrate are currently attracting attention. In this study, methanol was used as a co-substrate with CO2 to enhance butyrate production in MES. Feeding with CO2 and methanol resulted in the highest butyrate production rates and titres of 0.36 ± 0.01 g L-1 d-1 and 8.6 ± 0.2 g L-1, respectively, outperforming reactors with only CO2 feeding (0.20 ± 0.03 g L-1 d-1 and 5.2 ± 0.1 g L-1, respectively). Methanol acted as electron donor and as carbon source, both of which contributed ca. 50% of the carbon in the products. Eubacterium was the dominant genus with 52.6 ± 2.5% relative abundance. Thus, we demonstrate attractive route for the use of the C1 substrates, CO2 and methanol, to produce mainly butyrate. KEY POINTS: • Butyrate was the main product from methanol and CO2 in MES • Methanol acted as both carbon and electron source in MES • Eubacterium dominating microbial culture was enriched in MES.
Collapse
Affiliation(s)
- Hui Yao
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Johanna M Rinta-Kanto
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Igor Vassilev
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland
| | - Marika Kokko
- Faculty of Engineering and Natural Sciences, Tampere University, Korkeakoulunkatu 8, 33720, Tampere, Finland.
| |
Collapse
|
5
|
Siti Farah Norasyikeen SO, Ngui R, Syaza Zafirah AR, Md Zoqratt MZH, Eng WWH, Ayub Q, Amin Nordin S, Narcisse Mary Sither Joseph V, Musa S, Lim YAL. Study on intestinal parasitic infections and gut microbiota in cancer patients at a tertiary teaching hospital in Malaysia. Sci Rep 2024; 14:13650. [PMID: 38871760 DOI: 10.1038/s41598-024-59969-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 04/17/2024] [Indexed: 06/15/2024] Open
Abstract
Intestinal parasitic infections (IPIs) can lead to significant morbidity and mortality in cancer patients. While they are unlikely to cause severe disease and are self-limiting in healthy individuals, cancer patients are especially susceptible to opportunistic parasitic infections. The gut microbiota plays a crucial role in various aspects of health, including immune regulation and metabolic processes. Parasites occupy the same environment as bacteria in the gut. Recent research suggests intestinal parasites can disrupt the normal balance of the gut microbiota. However, there is limited understanding of this co-infection dynamic among cancer patients in Malaysia. A study was conducted to determine the prevalence and relationship between intestinal parasites and gut microbiota composition in cancer patients. Stool samples from 134 cancer patients undergoing active treatment or newly diagnosed were collected and examined for the presence of intestinal parasites and gut microbiota composition. The study also involved 17 healthy individuals for comparison and control. Sequencing with 16S RNA at the V3-V4 region was used to determine the gut microbial composition between infected and non-infected cancer patients and healthy control subjects. The overall prevalence of IPIs among cancer patients was found to be 32.8%. Microsporidia spp. Accounted for the highest percentage at 20.1%, followed by Entamoeba spp. (3.7%), Cryptosporidium spp. (3.0%), Cyclospora spp. (2.2%), and Ascaris lumbricoides (0.8%). None of the health control subjects tested positive for intestinal parasites. The sequencing data analysis revealed that the gut microbiota diversity and composition were significantly different in cancer patients than in healthy controls (p < 0.001). A significant dissimilarity was observed in the bacterial composition between parasite-infected and non-infected patients based on Bray-Curtis (p = 0.041) and Jaccard (p = 0.021) measurements. Bacteria from the genus Enterococcus were enriched in the parasite-infected groups, while Faecalibacterium prausnitzii reduced compared to non-infected and control groups. Further analysis between different IPIs and non-infected individuals demonstrated a noteworthy variation in Entamoeba-infected (unweighted UniFrac: p = 0.008), Cryptosporidium-infected (Bray-Curtis: p = 0.034) and microsporidia-infected (unweighted: p = 0.026; weighted: p = 0.019; Jaccard: p = 0.031) samples. No significant dissimilarity was observed between Cyclospora-infected groups and non-infected groups. Specifically, patients infected with Cryptosporidium and Entamoeba showed increased obligate anaerobic bacteria. Clostridiales were enriched with Entamoeba infections, whereas those from Coriobacteriales decreased. Bacteroidales and Clostridium were found in higher abundance in the gut microbiota with Cryptosporidium infection, while Bacillales decreased. Additionally, bacteria from the genus Enterococcus were enriched in microsporidia-infected patients. In contrast, bacteria from the Clostridiales order, Faecalibacterium, Parabacteroides, Collinsella, Ruminococcus, and Sporosarcina decreased compared to the non-infected groups. These findings underscore the importance of understanding and managing the interactions between intestinal parasites and gut microbiota for improved outcomes in cancer patients.
Collapse
Affiliation(s)
- Sidi Omar Siti Farah Norasyikeen
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Malaysia
| | - Romano Ngui
- Department of Paraclinical Sciences, Faculty of Medicine and Health Sciences, Universiti Malaysia Sarawak, 94300, Kota Samarahan, Malaysia.
| | - Ab Rahman Syaza Zafirah
- Department of Paediatrics, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | | | - Wilhelm Wei Han Eng
- Monash University Malaysia Genomics Facility, Monash University Malaysia, 47500, Subang Jaya, Malaysia
| | - Qasim Ayub
- Monash University Malaysia Genomics Facility, Monash University Malaysia, 47500, Subang Jaya, Malaysia
| | - Syafinaz Amin Nordin
- Department of Microbiology, Faculty of Medicine & Health Sciences, Universiti Putra Malaysia, 43400, Serdang, Malaysia
| | | | - Sabri Musa
- Department of Children's Dentistry and Orthodontics, Faculty of Dentistry, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| | - Yvonne Ai Lian Lim
- Department of Parasitology, Faculty of Medicine, Universiti Malaya, 50603, Kuala Lumpur, Malaysia
| |
Collapse
|
6
|
Yang X, Huang J, Peng J, Wang P, Wong FS, Wang R, Wang D, Wen L. Gut microbiota from B-cell-specific TLR9-deficient NOD mice promote IL-10 + Breg cells and protect against T1D. Front Immunol 2024; 15:1413177. [PMID: 38903498 PMCID: PMC11187306 DOI: 10.3389/fimmu.2024.1413177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Accepted: 05/22/2024] [Indexed: 06/22/2024] Open
Abstract
Introduction Type 1 diabetes (T1D) is an autoimmune disease characterized by the destruction of insulin-producing β cells. Toll-like receptor 9 (TLR9) plays a role in autoimmune diseases, and B cell-specific TLR9 deficiency delays T1D development. Gut microbiota are implicated in T1D, although the relationship is complex. However, the impact of B cell-specific deficiency of TLR9 on intestinal microbiota and the impact of altered intestinal microbiota on the development of T1D are unclear. Objectives This study investigated how gut microbiota and the intestinal barrier contribute to T1D development in B cell-specific TLR9-deficient NOD mice. Additionally, this study explored the role of microbiota in immune regulation and T1D onset. Methods The study assessed gut permeability, gene expression related to gut barrier integrity, and gut microbiota composition. Antibiotics depleted gut microbiota, and fecal samples were transferred to germ-free mice. The study also examined IL-10 production, Breg cell differentiation, and their impact on T1D development. Results B cell-specific TLR9-deficient NOD mice exhibited increased gut permeability and downregulated gut barrier-related gene expression. Antibiotics restored gut permeability, suggesting microbiota influence. Altered microbiota were enriched in Lachnospiraceae, known for mucin degradation. Transferring this microbiota to germ-free mice increased gut permeability and promoted IL-10-expressing Breg cells. Rag-/- mice transplanted with fecal samples from Tlr9 fl/fl Cd19-Cre+ mice showed delayed diabetes onset, indicating microbiota's impact. Conclusion B cell-specific TLR9 deficiency alters gut microbiota, increasing gut permeability and promoting IL-10-expressing Breg cells, which delay T1D. This study uncovers a link between TLR9, gut microbiota, and immune regulation in T1D, with implications for microbiota-targeted T1D therapies.
Collapse
Affiliation(s)
- Xin Yang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Juan Huang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Jian Peng
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| | - Pai Wang
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
- Department of Gastrocolorectal Surgery, General Surgery Center, The First Hospital of Jilin University, Changchun, Jilin, China
| | - F. Susan Wong
- Division of Infection and Immunity, Cardiff University School of Medicine, Cardiff, United Kingdom
| | - Ruirui Wang
- Shanghai Innovation Center of Traditional Chinese Medicine (TCM) Health Service, Shanghai University of Traditional Chinese Medicine, Shanghai, China
| | - Dapeng Wang
- Department of Food Science and Technology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Li Wen
- Section of Endocrinology, Internal Medicine, School of Medicine, Yale University, New Haven, CT, United States
| |
Collapse
|
7
|
Takada Y, Kanavillil N. Hierarchical diversity partitioning of microscopic epibiont community on intertidal molluscan shells and inert surfaces over three geographic regions in Japan. Oecologia 2024:10.1007/s00442-024-05575-2. [PMID: 38831021 DOI: 10.1007/s00442-024-05575-2] [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: 10/30/2023] [Accepted: 05/27/2024] [Indexed: 06/05/2024]
Abstract
Microscopic epibionts on molluscan shells are a component of the biodiversity of intertidal coastal areas. Because molluscan shells are discrete habitats for the epibiont community, and the molluscan basibionts belong to the local community, epibiont diversity can be evaluated hierarchically by basibiont categories including species. To evaluate the structure of epibiont diversity and effects of taxonomic resolution on the evaluation, epibionts on molluscan shells and inert surfaces were investigated at three geographically distant sites in Japan. In total, 94 species-level taxonomic units of epibionts were obtained from 31 basibiont molluscan species and inert surfaces (plastics and rock chips). The density and the species richness at the site of the lowest latitude were significantly lower than those at the other sites. The epibiont community differed between the three sites, although the major portion of the epibionts were diatoms. Between-site diversity contributed most of the total diversity of the species richness and Simpson diversity in the five levels of the hierarchical partitioning: sample (individual basibiont), basibiont species (molluscan species), surface group (bivalves, chitons + limpets, and globose gastropods), site, and the total. The taxonomic resolution did not markedly affect the variability of communities between the three sites, although the taxon richness was reduced to 51 in the genus-level analysis. The lower taxonomic resolution (genus level); however, increased the contribution of the within-sample and decreased the contribution of β diversities at the higher hierarchies, leading to a possible overestimation of biotic homogenization between the communities.
Collapse
Affiliation(s)
- Yoshitake Takada
- Japan Fisheries Research and Education Agency, Fukuura 2-12-4, Kanazawa, Yokohama, Kanagawa, 236-8648, Japan.
| | - Nandakumar Kanavillil
- Department of Sustainability Sciences, Lakehead University, 500 University Ave, Orillia, ON, L3V 0B9, Canada
| |
Collapse
|
8
|
Oliveira HKLG, Miranda PN, Ortega JCG, Morato EF. Vertical Stratification of Solitary Bees and Wasps in an Urban Forest from the Brazilian Amazon. NEOTROPICAL ENTOMOLOGY 2024; 53:552-567. [PMID: 38684598 DOI: 10.1007/s13744-024-01142-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024]
Abstract
Solitary bees and wasps that nest in cavities in tree trunks are important components of terrestrial ecosystems, providing pollination services, and in the case of wasps, the regulation of their prey populations. However, little is known about the vertical strata where bees and wasps build their nests. This is especially the case of urban forest remnants in the Amazon, which is relevant in the context of the global crisis in insect losses. We investigated the existence of vertical stratification in the nesting of solitary bees and wasps in an urban forest in Rio Branco, state of Acre, in the western Brazilian Amazon. We focused on whether wood temperature, ants, and termites are predictors of bee and wasp nesting. We sampled bee and wasp nests in the forest using trap-nests made with wooden blocks containing cavities with three different diameters for twelve months. Trap-nests were installed randomly at three heights in the forest. We collected 145 nests of 25 species, belonging to 11 genera and 6 families. A higher number of nests and species were collected in the upper stratum of the forest, strengthening the hypothesis that there is vertical stratification in the assemblage of solitary bees and wasps. Wood surface temperature and termite attacks on trap-nests were significantly different between strata, which may explain the vertical stratification of bee and wasp assemblages. Considering the importance of these insects for tropical forest ecosystems, the conservation of structurally complex and stratified forests is of paramount importance to maintain the diversity of this insect group.
Collapse
Affiliation(s)
| | | | | | - Elder Ferreira Morato
- Laboratório de Ecologia de Insetos, Centro de Ciências Biológicas e da Natureza, Universidade Federal do Acre - UFAC, Rio Branco, AC, Brazil
| |
Collapse
|
9
|
Browning BD, Kirkland AE, Green R, Liu H, Glover JS, Ticer TD, Engevik MA, Alekseyenko AV, Ferguson PL, Tomko RL, Squeglia LM. Adolescent alcohol use is associated with differences in the diversity and composition of the oral microbiome. ALCOHOL, CLINICAL & EXPERIMENTAL RESEARCH 2024; 48:1025-1035. [PMID: 38631877 PMCID: PMC11178446 DOI: 10.1111/acer.15331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 03/22/2024] [Accepted: 04/03/2024] [Indexed: 04/19/2024]
Abstract
BACKGROUND Adolescence is a sensitive stage of oral microbial development that often coincides with the initiation and escalation of alcohol use. Thus, adolescents may be particularly susceptible to alcohol-induced alterations in the oral microbiome, though minimal research has been done in this area. Understanding the connection between the oral microbiome and alcohol use during adolescence is important to understand fully the biological consequences of alcohol use to mitigate potential adverse outcomes. METHODS Saliva samples were collected from adolescents aged 17-19 who used alcohol heavily (n = 21, 52.4% female) and those who did not use alcohol or any other substances (n = 18, 44.4% female). We utilized 16S rRNA sequencing to examine differences in microbial diversity and composition between the groups. RESULTS For alpha diversity, evenness was significantly lower in the drinking group than the control group as indicated by Pielou's evenness, Shannon, and Simpson indices. There were no statistically significant findings for beta diversity. Differential abundance analyses revealed higher abundances of Rothia and Corynebacterium in the alcohol-using group using both centered-log-ratio and relative abundance normalization. These genera are known for their high capacity to convert alcohol into acetaldehyde, a toxic metabolite reported to play a role in the neurobiological effects of alcohol. An unclassified Clostridia UCG-014, Streptobacillus, Comamonas, unclassified Lachnospiraceae, and Parvimonas were also identified as significantly different between groups when using only one of the normalization techniques. CONCLUSIONS This is the first study designed specifically to compare the oral microbiome of adolescents who use alcohol with that of control participants. Our findings reveal distinct alcohol-related differences in microbial composition and taxon abundance, emphasizing the importance of understanding the impact on the oral microbiome of alcohol use during adolescence. Because the oral microbiome is malleable, this study provides foundational work for future prevention and intervention studies.
Collapse
Affiliation(s)
- Brittney D. Browning
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
- Department of Neuroscience, Medical University of South Carolina, Charleston, SC, USA
| | - Anna E. Kirkland
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Rejoyce Green
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Helen Liu
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Janiece S. Glover
- Department of Regenerative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Taylor D. Ticer
- Department of Regenerative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | - Mindy A. Engevik
- Department of Regenerative Medicine, Medical University of South Carolina, Charleston, SC, USA
| | | | - Pamela L. Ferguson
- Department of Public Health Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Rachel L. Tomko
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| | - Lindsay M. Squeglia
- Department of Psychiatry and Behavioral Sciences, Medical University of South Carolina, Charleston, SC, USA
| |
Collapse
|
10
|
Scales BS, Hassenrück C, Moldaenke L, Hassa J, Rückert-Reed C, Rummel C, Völkner C, Rynek R, Busche T, Kalinowski J, Jahnke A, Schmitt-Jansen M, Wendt-Potthoff K, Oberbeckmann S. Hunting for pigments in bacterial settlers of the Great Pacific Garbage Patch. Environ Microbiol 2024; 26:e16639. [PMID: 38899733 DOI: 10.1111/1462-2920.16639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 04/30/2024] [Indexed: 06/21/2024]
Abstract
The Great Pacific Garbage Patch, a significant collection of plastic introduced by human activities, provides an ideal environment to study bacterial lifestyles on plastic substrates. We proposed that bacteria colonizing the floating plastic debris would develop strategies to deal with the ultraviolet-exposed substrate, such as the production of antioxidant pigments. We observed a variety of pigmentation in 67 strains that were directly cultivated from plastic pieces sampled from the Garbage Patch. The genomic analysis of four representative strains, each distinct in taxonomy, revealed multiple pathways for carotenoid production. These pathways include those that produce less common carotenoids and a cluster of photosynthetic genes. This cluster appears to originate from a potentially new species of the Rhodobacteraceae family. This represents the first report of an aerobic anoxygenic photoheterotrophic bacterium from plastic biofilms. Spectral analysis showed that the bacteria actively produce carotenoids, such as beta-carotene and beta-cryptoxanthin, and bacteriochlorophyll a. Furthermore, we discovered that the genetic ability to synthesize carotenoids is more common in plastic biofilms than in the surrounding water communities. Our findings suggest that plastic biofilms could be an overlooked source of bacteria-produced carotenoids, including rare forms. It also suggests that photoreactive molecules might play a crucial role in bacterial biofilm communities in surface water.
Collapse
Affiliation(s)
- Brittan S Scales
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Christiane Hassenrück
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
| | - Lynn Moldaenke
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Julia Hassa
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | | | - Christoph Rummel
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Corinna Völkner
- Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Robby Rynek
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
| | - Tobias Busche
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Jörn Kalinowski
- Center for Biotechnology (CeBiTec), Universität Bielefeld, Bielefeld, Germany
| | - Annika Jahnke
- Helmholtz Centre for Environmental Research - UFZ, Leipzig, Germany
- Institute for Environmental Research, RWTH Aachen University, Aachen, Germany
| | | | | | - Sonja Oberbeckmann
- Department of Biological Oceanography, Leibniz Institute for Baltic Sea Research Warnemünde, Rostock, Germany
- Federal Institute for Materials Research and Testing (BAM), Berlin, Germany
| |
Collapse
|
11
|
Fukasawa Y, Kitabatake H. Factors associated with seedling establishment on logs of different fungal decay types-A seed-sowing experiment. Ecol Evol 2024; 14:e11508. [PMID: 38835527 PMCID: PMC11148398 DOI: 10.1002/ece3.11508] [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: 01/08/2024] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 06/06/2024] Open
Abstract
Wood decay fungi alter the abiotic and biotic properties of deadwood, which are important as nurse logs for seedling regeneration. However, the relationship between fungal decay type and seedling performance has not been evaluated experimentally. In this study, we examined the germination, growth, and survival of six arbuscular mycorrhizal (AM) and six ectomycorrhizal (ECM) tree species on three substrates (pine logs with brown and white rot and soil) by conducting seed-sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. Analysis using ribosomal DNA internal transcribed spacer 1 (rDNA ITS1) sequencing revealed that the fungal community was significantly different across three substrates. The richness of operational taxonomic units (OTUs) of AM and ECM fungi was the largest on brown rot logs and soil, respectively. The substrate significantly affected the seedling performance when comparing wood decay types, but these were not consistent across the mycorrhizal status of the seedlings. Nevertheless, seedlings of some AM trees showed better growth and enhanced mycorrhizal colonization on brown rot logs than on white rot logs. The wood decay type influenced fungal communities in the logs and the performance of some seedling species partly by different mycorrhizal colonization rates. However, the effect was seedling species dependent and showed no apparent difference between AM and ECM trees.
Collapse
Affiliation(s)
- Yu Fukasawa
- Laboratory of Forest Ecology, Graduate School of Agricultural Science Tohoku University Osaki Japan
| | - Hiroyuki Kitabatake
- Laboratory of Forest Ecology, Graduate School of Agricultural Science Tohoku University Osaki Japan
| |
Collapse
|
12
|
Alfonso P, Butković A, Fernández R, Riesgo A, Elena SF. Unveiling the hidden viromes across the animal tree of life: insights from a taxonomic classification pipeline applied to invertebrates of 31 metazoan phyla. mSystems 2024; 9:e0012424. [PMID: 38651902 PMCID: PMC11097642 DOI: 10.1128/msystems.00124-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2024] [Accepted: 03/26/2024] [Indexed: 04/25/2024] Open
Abstract
Invertebrates constitute the majority of animal species on Earth, including most disease-causing agents or vectors, with more diverse viromes when compared to vertebrates. Recent advancements in high-throughput sequencing have significantly expanded our understanding of invertebrate viruses, yet this knowledge remains biased toward a few well-studied animal lineages. In this study, we analyze invertebrate DNA and RNA viromes for 31 phyla using 417 publicly available RNA-Seq data sets from diverse environments in the marine-terrestrial and marine-freshwater gradients. This study aims to (i) estimate virome compositions at the family level for the first time across the animal tree of life, including the first exploration of the virome in several phyla, (ii) quantify the diversity of invertebrate viromes and characterize the structure of invertebrate-virus infection networks, and (iii) investigate host phylum and habitat influence on virome differences. Results showed that a set of few viral families of eukaryotes, comprising Retroviridae, Flaviviridae, and several families of giant DNA viruses, were ubiquitous and highly abundant. Nevertheless, some differences emerged between phyla, revealing for instance a less diverse virome in Ctenophora compared to the other animal phyla. Compositional analysis of the viromes showed that the host phylum explained over five times more variance in composition than its habitat. Moreover, significant similarities were observed between the viromes of some phylogenetically related phyla, which could highlight the influence of co-evolution in shaping invertebrate viromes.IMPORTANCEThis study significantly enhances our understanding of the global animal virome by characterizing the viromes of previously unexamined invertebrate lineages from a large number of animal phyla. It showcases the great diversity of viromes within each phylum and investigates the role of habitat shaping animal viral communities. Furthermore, our research identifies dominant virus families in invertebrates and distinguishes phyla with analogous viromes. This study sets the road toward a deeper understanding of the virome across the animal tree of life.
Collapse
Affiliation(s)
- Pau Alfonso
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
| | - Anamarija Butković
- Institut Pasteur, Université Paris Cité, CNRS UMR6047 Archaeal Virology Unit, Paris, France
| | - Rosa Fernández
- Instituto de Biología Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Ana Riesgo
- Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
- Department of Life Sciences, Natural History Museum of London, London, United Kingdom
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (CSIC-Universitat de València), Paterna, València, Spain
- The Santa Fe Institute, Santa Fe, New Mexico, USA
| |
Collapse
|
13
|
Meza-Buendia AK, Aparicio-Trejo OE, Díaz F, Pedraza-Chaverri J, Álvarez-Delgado C, Rosas C. Climate change consequences on the systemic heart of female Octopus maya: oxidative phosphorylation assessment and the antioxidant system. Biol Open 2024; 13:bio060103. [PMID: 38752595 PMCID: PMC11155352 DOI: 10.1242/bio.060103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 04/05/2024] [Indexed: 06/09/2024] Open
Abstract
There is evidence that indicates that temperature modulates the reproduction of the tropical species Octopus maya, through the over- or under-expression of many genes in the brain. If the oxygen supply to the brain depends on the circulatory system, how temperature affects different tissues will begin in the heart, responsible for pumping the oxygen to tissues. The present study examines the impact of heat stress on the mitochondrial function of the systemic heart of adult O. maya. The mitochondrial metabolism and antioxidant defense system were measured in the systemic heart tissue of female organisms acclimated to different temperatures (24, 26, and 30°C). The results show that acclimation temperature affects respiratory State 3 and State 4o (oligomycin-induced) with higher values observed in females acclimated at 26°C. The antioxidant defense system is also affected by acclimation temperature with significant differences observed in superoxide dismutase, glutathione S-transferase activities, and glutathione levels. The results suggest that high temperatures (30°C) could exert physical limitations on the circulatory system through the heart pumping, affecting nutrient and oxygen transport to other tissues, including the brain, which exerts control over the reproductive system. The role of the cardiovascular system in supporting aerobic metabolism in octopus females is discussed.
Collapse
Affiliation(s)
- Ana Karen Meza-Buendia
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860Ensenada, Baja California, México
| | - Omar Emiliano Aparicio-Trejo
- Departamento de Fisiopatología Cardio-Renal, Instituto Nacional de Cardiología “Ignacio Chávez”, 14080 Ciudad de México, México
| | - Fernando Díaz
- Departamento de Biotecnología Marina, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860Ensenada, Baja California, México
| | - José Pedraza-Chaverri
- Laboratorio F-315, Departamento de Biología, Facultad de Química, Universidad Nacional Autónoma de México, 04510, Ciudad de México, México
| | - Carolina Álvarez-Delgado
- Departamento de Innovación Biomédica, Centro de Investigación Científica y de Educación Superior de Ensenada, 22860 Ensenada, Baja California, México
| | - Carlos Rosas
- Laboratorio de Ecofisiología Aplicada, Unidad Multidisciplinaria de Docencia e Investigación, de Sisal, Facultad de Ciencias, Universidad Nacional Autónoma de México, 97356 Puerto de Abrigo, Sisal, Yucatán, México
| |
Collapse
|
14
|
Shah AS, Hsu PC, Chisholm C, Podolyan A, Cameron K, Luo J, Stenger R, Carrick S, Hu W, Ferguson SA, Wei W, Shen J, Zhang L, Liu H, Zhao T, Wei W, Ding W, Pan H, Liu Y, Li B, Du J, Di HJ. Nitrification inhibitor chlorate and nitrogen substrates differentially affect comammox Nitrospira in a grassland soil. Front Microbiol 2024; 15:1392090. [PMID: 38808273 PMCID: PMC11130707 DOI: 10.3389/fmicb.2024.1392090] [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: 02/26/2024] [Accepted: 04/26/2024] [Indexed: 05/30/2024] Open
Abstract
Introduction Through the combined use of two nitrification inhibitors, Dicyandiamide (DCD) and chlorate with nitrogen amendment, this study aimed to investigate the contribution of comammox Nitrospira clade B, ammonia oxidizing bacteria (AOB) and archaea (AOA) to nitrification in a high fertility grassland soil, in a 90-day incubation study. Methods The soil was treated with nitrogen (N) at three levels: 0 mg-N kg-1 soil, 50 mg-N kg-1 soil, and 700 mg-N kg-1 soil, with or without the two nitrification inhibitors. The abundance of comammox Nitrospira, AOA, AOB, and nitrite oxidising bacteria (NOB) was measured using qPCR. The comammox Nitrospira community structure was assessed using Illumina sequencing. Results and Discussion The results showed that the application of chlorate inhibited the oxidation of both NH4+ and NO2- in all three nitrogen treatments. The application of chlorate significantly reduced the abundance of comammox Nitrospira amoA and nxrB genes across the 90-day experimental period. Chlorate also had a significant effect on the beta diversity (Bray-Curtis dissimilarity) of the comammox Nitrospira clade B community. Whilst AOB grew in response to the N substrate additions and were inhibited by both inhibitors, AOA showed litle or no response to either the N substrate or inhibitor treatments. In contrast, comammox Nitrospira clade B were inhibited by the high ammonium concentrations released from the urine substrates. These results demonstrate the differential and niche responses of the three ammonia oxidising communities to N substrate additions and nitrification inhibitor treatments. Further research is needed to investigate the specificity of the two inhibitors on the different ammonia oxidising communities.
Collapse
Affiliation(s)
- Anish S. Shah
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Pei-Chun Hsu
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Chris Chisholm
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Andriy Podolyan
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | - Keith Cameron
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| | | | - Roland Stenger
- Lincoln Agritech, Ruakura Research Centre, Hamilton, New Zealand
| | - Sam Carrick
- Manaaki Whenua - Landcare Research, Lincoln, New Zealand
| | - Wei Hu
- The New Zealand Institute for Plant and Food Research, Lincoln, New Zealand
| | - Scott A. Ferguson
- Department of Microbiology, University of Otago, Dunedin, New Zealand
| | - Wenhua Wei
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | | | - Limei Zhang
- Research Centre for Eco-Environmental Science, Chinese Academy of Sciences, Beijing, China
| | - Hongbin Liu
- Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tongke Zhao
- Beijing Academy of Agriculture and Forestry Sciences, Beijing, China
| | - Wenxue Wei
- Institute of Subtropical Agricultural Ecology, Chinese Academy of Sciences, Changsha, China
| | - Weixin Ding
- Institute of Soil Science, Chinese Academy of Sciences, Nanjing, China
| | - Hong Pan
- College of Natural Resources and Environment, Shandong Agricultural University, Taian, China
| | - Yimeng Liu
- Centre for Innovation and Development, Beijing Normal University, Zhuhai, China
| | - Bowen Li
- College of Natural Resources and Environment, Hebei Agricultural University, Baoding, China
| | - Jianjun Du
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Hong J. Di
- Centre for Soil and Environmental Research, Lincoln University, Lincoln, New Zealand
| |
Collapse
|
15
|
Shigyo N, Umeki K, Hirao T. Soil microbial identity explains home-field advantage for litter decomposition. THE NEW PHYTOLOGIST 2024. [PMID: 38736202 DOI: 10.1111/nph.19769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 03/25/2024] [Indexed: 05/14/2024]
Abstract
Unraveling the mechanisms of home-field advantage (HFA) is essential to gain a complete understanding of litter decomposition processes. However, knowledge of the relationships between HFA effects and microbial communities is lacking. To examine HFA effects on litter decomposition, we identified the microbial communities and conducted a reciprocal transplant experiment, including all possible combinations of soil and litter, between sites at two elevations in cool-temperate forests. Soil origin, rather than HFA, was an important factor in controlling litter decomposition processes. Microbiome-wide association analyses identified litter fungi and bacteria specific to the source soil, which completely differed at a low taxonomic level between litter types. The relative abundance of these microbes specific to source soil was positively correlated with litter mass loss. The results indicated that the unique relationships between plant litter and soil microbes through plant-soil linkages drive litter decomposition processes. In the short term, soil disturbances resulting from land-use changes have the potential to disrupt the effect of soil origin and hinder the advancement of litter decomposition. These findings contribute to an understanding of HFA mechanisms and the impacts of land-use change on decomposition processes in forest ecosystems.
Collapse
Affiliation(s)
- Nobuhiko Shigyo
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
| | - Kiyoshi Umeki
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo, Chiba, 271-8510, Japan
| | - Toshihide Hirao
- The University of Tokyo Chichibu Forest, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-49 Hinoda-machi, Chichibu, Saitama, 368-0034, Japan
| |
Collapse
|
16
|
Mahalak KK, Liu L, Bobokalonov J, Narrowe AB, Firrman J, Bittinger K, Hu W, Jones SM, Moustafa AM. Supplementation with soluble or insoluble rice-bran fibers increases short-chain fatty acid producing bacteria in the gut microbiota in vitro. Front Nutr 2024; 11:1304045. [PMID: 38798771 PMCID: PMC11116651 DOI: 10.3389/fnut.2024.1304045] [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: 09/28/2023] [Accepted: 04/11/2024] [Indexed: 05/29/2024] Open
Abstract
Introduction Studies have shown that a diet high in fiber and prebiotics has a positive impact on human health due largely to the fermentation of these compounds by the gut microbiota. One underutilized source of fiber may be rice bran, a waste product of rice processing that is used most frequently as an additive to livestock feed but may be a good source of fibers and other phenolic compounds as a human diet supplement. Previous studies focused on specific compounds extracted from rice bran showed that soluble fibers extracted from rice bran can improve glucose response and reduce weight gain in mouse models. However, less is known about changes in the human gut microbiota in response to regular rice bran consumption. Methods In this study, we used a Simulator of the Human Intestinal Microbial Ecology (SHIME®) to cultivate the human gut microbiota of 3 different donors in conditions containing either soluble or insoluble fiber fractions from rice bran. Using 16S rRNA amplicon sequencing and targeted metabolomics via Gas Chromatography-Mass Spectrometry, we explored how gut microbial communities developed provided different supplemental fiber sources. Results We found that insoluble and soluble fiber fractions increased short-chain fatty acid production, indicating that both fractions were fermented. However, there were differences in response between donors, for example the gut microbiota from donor 1 increased acetic acid production with both fiber types compared with control; whereas for donors 2 and 3, butanoic acid production increased with ISF and SF supplementation. Both soluble and insoluble rice bran fractions increased the abundance of Bifidobacterium and Lachnospiraceae taxa. Discussion Overall, analysis of the effect of soluble and insoluble rice bran fractions on the human in vitro gut microbiota and the metabolites produced revealed individually variant responses to these prebiotics.
Collapse
Affiliation(s)
- Karley K. Mahalak
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - LinShu Liu
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Jamshed Bobokalonov
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
- V. I. Nikitin Institute of Chemistry, National Academy of Sciences, Dushanbe, Tajikistan
| | - Adrienne B. Narrowe
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Jenni Firrman
- Dairy and Functional Foods Research Unit, Eastern Regional Research Center, Agricultural Research Service, United States Department of Agriculture, Wyndmoor, PA, United States
| | - Kyle Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Weiming Hu
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Steven M. Jones
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
| | - Ahmed M. Moustafa
- Division of Gastroenterology, Hepatology, and Nutrition, The Children’s Hospital of Philadelphia, Philadelphia, PA, United States
- Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| |
Collapse
|
17
|
Orlandi Neto A, Franceschini L, Dias JHP, Ribeiro CDS, Ramos IP. Endoparasitic helminth fauna and diet of Geophagus sveni (Pisces) in Upper Paraná River basin. Parasitol Res 2024; 123:208. [PMID: 38724709 DOI: 10.1007/s00436-024-08222-0] [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: 02/16/2024] [Accepted: 04/24/2024] [Indexed: 06/04/2024]
Abstract
In freshwater ecosystems, parasite infection patterns are influenced by factors including spatial-temporal variations, host diet, and habitat. Fish often change diets, affecting their parasite communities. This study focused on non-native host fish Geophagus sveni, aiming to characterize diet and endoparasitic helminth fauna patterns in the invaded area, investigating spatial and seasonal possible differences of endoparasite infections and correlating with host diet, in São José dos Dourados River and Tietê River areas. The host fish were collected in these areas during the dry and rainy season using gillnets. The endoparasites were collected and preserved in alcohol and identified using taxonomic methods, and stomach contents were examined for diet analysis. Parasitism descriptors were calculated and evaluated spatially and seasonally by ANOVA and the Kruskal-Wallis tests. PERMANOVA assessed G. sveni diet differences, and RDA correlated the endohelminth abundance with the host diet. Two endoparasites were recorded: metacercariae of Austrodiplostomum compactum (Trematoda) and larvae and adults of Raphidascaris (Sprentascaris) lanfrediae (Nematoda). Spatial differences were observed for the mean abundance and prevalence of R. (S.) lanfrediae and A. compactum prevalence. Seasonal variations of parasitic descriptors occurred for the nematode in the Tietê River area. The detritus and aquatic insects were the most consumed items by G. sveni. Detritus consumption positively correlates with nematode abundance. The findings indicate that factors such as artificial channels and rainfall, which can influence resource availability, may affect the fish's diet and potentially influence the structure of its endoparasite community. The study emphasizes the importance of understanding trophic chain-transmitted parasites and calls for further research in Neotropical environments.
Collapse
Affiliation(s)
- Aymar Orlandi Neto
- Institute of Biosciences of Botucatu, São Paulo State University (UNESP), Botucatu, Brazil.
| | - Lidiane Franceschini
- Institute of Biosciences, Humanities and Exact Sciences, São Paulo State University (UNESP), São José Do Rio Preto, Brazil
| | | | | | - Igor Paiva Ramos
- School of Engineering, São Paulo State University (UNESP), Ilha Solteira, Brazil
| |
Collapse
|
18
|
Mühlen S, Heroven AK, Elxnat B, Kahl S, Pieper DH, Dersch P. Infection and antibiotic-associated changes in the fecal microbiota of C. rodentium ϕ stx2dact-infected C57BL/6 mice. Antimicrob Agents Chemother 2024; 68:e0005724. [PMID: 38526080 PMCID: PMC11064522 DOI: 10.1128/aac.00057-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 02/24/2024] [Indexed: 03/26/2024] Open
Abstract
Enterohemorrhagic Escherichia coli causes watery to bloody diarrhea, which may progress to hemorrhagic colitis and hemolytic-uremic syndrome. While early studies suggested that antibiotic treatment may worsen the pathology of an enterohemorrhagic Escherichia coli (EHEC) infection, recent work has shown that certain non-Shiga toxin-inducing antibiotics avert disease progression. Unfortunately, both intestinal bacterial infections and antibiotic treatment are associated with dysbiosis. This can alleviate colonization resistance, facilitate secondary infections, and potentially lead to more severe illness. To address the consequences in the context of an EHEC infection, we used the established mouse infection model organism Citrobacter rodentium ϕstx2dact and monitored changes in fecal microbiota composition during infection and antibiotic treatment. C. rodentium ϕstx2dact infection resulted in minor changes compared to antibiotic treatment. The infection caused clear alterations in the microbial community, leading mainly to a reduction of Muribaculaceae and a transient increase in Enterobacteriaceae distinct from Citrobacter. Antibiotic treatments of the infection resulted in marked and distinct variations in microbiota composition, diversity, and dispersion. Enrofloxacin and trimethoprim/sulfamethoxazole, which did not prevent Shiga toxin-mediated organ damage, had the least disruptive effects on the intestinal microbiota, while kanamycin and tetracycline, which rapidly cleared the infection without causing organ damage, caused a severe reduction in diversity. Kanamycin treatment resulted in the depletion of all but Bacteroidetes genera, whereas tetracycline effects on Clostridia were less severe. Together, these data highlight the need to address the impact of individual antibiotics in the clinical care of life-threatening infections and consider microbiota-regenerating therapies.IMPORTANCEUnderstanding the impact of antibiotic treatment on EHEC infections is crucial for appropriate clinical care. While discouraged by early studies, recent findings suggest certain antibiotics can impede disease progression. Here, we investigated the impact of individual antibiotics on the fecal microbiota in the context of an established EHEC mouse model using C. rodentium ϕstx2dact. The infection caused significant variations in the microbiota, leading to a transient increase in Enterobacteriaceae distinct from Citrobacter. However, these effects were minor compared to those observed for antibiotic treatments. Indeed, antibiotics that most efficiently cleared the infection also had the most detrimental effect on the fecal microbiota, causing a substantial reduction in microbial diversity. Conversely, antibiotics showing adverse effects or incomplete bacterial clearance had a reduced impact on microbiota composition and diversity. Taken together, our findings emphasize the delicate balance required to weigh the harmful effects of infection and antibiosis in treatment.
Collapse
Affiliation(s)
- Sabrina Mühlen
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, University of Münster, Münster, Germany
- German Centre for Infection Research (DZIF), partner site HZI, Braunschweig, and associated site University of Münster, Münster, Germany
- Department of Molecular Immunology, Ruhr-University Bochum, Bochum, Germany
| | - Ann Kathrin Heroven
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Bettina Elxnat
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Silke Kahl
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Dietmar H. Pieper
- Microbial Interactions and Processes, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Petra Dersch
- Department of Molecular Infection Biology, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute of Infectiology, University of Münster, Münster, Germany
- German Centre for Infection Research (DZIF), partner site HZI, Braunschweig, and associated site University of Münster, Münster, Germany
| |
Collapse
|
19
|
Tyrsin OY, Tyrsin DY, Nemenov DG, Ruzov AS, Odintsova VE, Koshechkin SI, D Amico L. Effect of Lactobacillus reuteri NCIMB 30351 drops on symptoms of infantile functional gastrointestinal disorders and gut microbiota in early infants: Results from a randomized, placebo-controlled clinical trial. Eur J Pediatr 2024; 183:2311-2324. [PMID: 38427038 DOI: 10.1007/s00431-024-05473-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 01/23/2024] [Accepted: 02/04/2024] [Indexed: 03/02/2024]
Abstract
Infantile functional gastrointestinal disorders, such as colic, constipation, diarrhea, and gastroesophageal reflux (regurgitation), often occur in early infancy and, representing one of the causes of significant parental anxiety, lead to a significant strain on the healthcare resources. In this study, we aimed to evaluate the effects of Lactobacillus reuteri drops (L. reuteri NCIMB 30351) on the symptoms of infantile colic, constipation, diarrhea, and gastroesophageal reflux, as well as on the levels of intestinal microbiota in full-term newborns during the first months of life. A randomized, placebo-controlled, single-masked (blinded), post-marketing clinical study was conducted in two clinical units-Children's City Clinical Hospital of Moscow and Medical Center "St. Andrew's Hospitals-NEBOLIT" from March 2020 to May 2022 in 90 infants aged from 1 to 4 months (mean age (± SD) 12.3 ± 5.09 weeks; 53.3% females, 46.7% males). Patients with colic, regurgitation (single symptom or combination of several symptoms), and constipation or diarrhea were randomly allocated in two parallel arms to receive either 5 drops (2 × 108 colony forming unit) of L. reuteri NCIMB 30351 (n = 60) or masked placebo (n = 30) for 25 consecutive days. Two treatment arms had equal numbers of patients with constipation and diarrhea (n = 30 each). Daily crying times and their duration, evacuations, and regurgitations were recorded in a structured diary. The levels of gut microbiota were analyzed by deep sequencing of bacterial 16S rRNA gene. Infants with colic receiving supplementary L. reuteri NCIMB 30351 for 25 days had significant reduction in the numbers of colic (change from baseline - 6.3 (7.34) vs - 3.0 (7.29) in placebo, P < 0.05) and numbers of crying cases and mean duration of crying (decrease from baseline - 144 (70.7) minutes, lower in the diarrhea subgroup than in constipation infants, compared with - 80 (58.9) in placebo, P < 0.0001), as well as regurgitation numbers (decreased by - 4.8 (2.49) with L. reuteri vs - 3 (7.74) with placebo). We also observed increased numbers of evacuations in infants with constipation (L. reuteri 2.2 (2.4) vs 0.9 (1.06) in placebo, P < 0.05). There was a remarkable reduction of evacuations in infants with diarrhea, while not statistically significant. The analysis of bacterial 16S rRNA gene in the collected samples showed that L. reuteri positively influences the proportions of prevalent species, while it negatively affects both conditionally pathogenic and commensal microbes. Additional in vitro test for formation of Clostridium colonies in the presence of the probiotic demonstrated that L. reuteri effectively inhibits the growth of pathogenic Clostridium species. No adverse events were reported in this study. Conclusion: The uptake of L. reuteri NCIMB 30351 leads to a significant reduction in the number of regurgitations, feeding-induced constipations, and diarrhea as well as mean daily numbers of crying and crying duration in infants during the first months of life. Our results suggest that L. reuteri NCIMB 30351 represents a safe and effective treatment for colic in newborns. Trial registration: ClinicalTrials.gov : NCT04262648. What is Known: • Infantile functional gastrointestinal disorders, such as colic, constipation, diarrhea, and gastroesophageal reflux (regurgitation), often occur in early infancy and, represent one of the causes of significant parental anxiety. • A number of studies have shown that both the composition and diversity of the intestinal microbiota play important roles in the development and function of the gastrointestinal tract. What is New: • The uptake of L. reuteri NCIMB 30351 leads to a significant reduction in the number of regurgitations, feeding-induced constipations, and diarrhea as well as mean daily numbers of crying and crying duration in infants during the first months of life. • L. reuteri positively influences the proportions of prevalent species, while it negatively affects both conditionally pathogenic and commensal microbes in gut microbiota.
Collapse
|
20
|
Paraskevopoulos AW, Sanders NJ, Resasco J. Temperature-driven homogenization of an ant community over 60 years in a montane ecosystem. Ecology 2024; 105:e4302. [PMID: 38594213 DOI: 10.1002/ecy.4302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/19/2023] [Accepted: 01/19/2024] [Indexed: 04/11/2024]
Abstract
Identifying the mechanisms underlying the changes in the distribution of species is critical to accurately predict how species have responded and will respond to climate change. Here, we take advantage of a late-1950s study on ant assemblages in a canyon near Boulder, Colorado, USA, to understand how and why species distributions have changed over a 60-year period. Community composition changed over 60 years with increasing compositional similarity among ant assemblages. Community composition differed significantly between the periods, with aspect and tree cover influencing composition. Species that foraged in broader temperature ranges became more widespread over the 60-year period. Our work highlights that shifts in community composition and biotic homogenization can occur even in undisturbed areas without strong habitat degradation. We also show the power of pairing historical and contemporary data and encourage more mechanistic studies to predict species changes under climate change.
Collapse
Affiliation(s)
- Anna W Paraskevopoulos
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Nathan J Sanders
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, USA
| | - Julian Resasco
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| |
Collapse
|
21
|
Siemering GS, Arriaga FJ, Cagle GA, Van Beek JM, Freedman ZB. Impacts of vegetable processing and cheese making effluent on soil microbial functional diversity, community structure, and denitrification potential of land treatment systems. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2024; 96:e11036. [PMID: 38740567 DOI: 10.1002/wer.11036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/16/2024] [Accepted: 04/20/2024] [Indexed: 05/16/2024]
Abstract
The cheese making and vegetable processing industries generate immense volumes of high-nitrogen wastewater that is often treated at rural facilities using land applications. Laboratory incubation results showed denitrification decreased with temperature in industry facility soils but remained high in soils from agricultural sites (75% at 2.1°C). 16S rRNA, phospholipid fatty acid (PLFA), and soil respiration analyses were conducted to investigate potential soil microbiome impacts. Biotic and abiotic system factor correlations showed no clear patterns explaining the divergent denitrification rates. In all three soil types at the phylum level, Actinobacteria, Proteobacteria, and Acidobacteria dominated, whereas at the class level, Nitrososphaeria and Alphaproteobacteria dominated, similar to denitrifying systems such as wetlands, wastewater resource recovery facilities, and wastewater-irrigated agricultural systems. Results show that potential denitrification drivers vary but lay the foundation to develop a better understanding of the key factors regulating denitrification in land application systems and protect local groundwater supplies. PRACTITIONER POINTS: Incubation study denitrification rates decreased as temperatures decreased, potentially leading to groundwater contamination issues during colder months. The three most dominant phyla for all systems are Actinobacteria, Proteobacteria, and Acidobacteria. The dominant class for all systems is Nitrosphaeria (phyla Crenarchaeota). No correlation patterns between denitrification rates and system biotic and abiotic factors were observed that explained system efficiency differences.
Collapse
Affiliation(s)
- Geoffrey S Siemering
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Francisco J Arriaga
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Grace A Cagle
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Joelie M Van Beek
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zachary B Freedman
- Department of Soil Science, University of Wisconsin-Madison, Madison, Wisconsin, USA
| |
Collapse
|
22
|
Mizuno T, Sato H, Itioka T. Foraging ants affect community composition and diversity of phyllosphere fungi on a myrmecophilous plants, Mallotus japonicus. Ecol Evol 2024; 14:e11423. [PMID: 38751826 PMCID: PMC11094773 DOI: 10.1002/ece3.11423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 04/06/2024] [Accepted: 05/02/2024] [Indexed: 05/18/2024] Open
Abstract
Many microorganisms inhabit the aboveground parts of plants (i.e. the phyllosphere), which mainly comprise leaves. Understanding the structure of phyllosphere microbial communities and their drivers is important because they influence host plant fitness and ecosystem functions. Despite the high prevalence of ant-plant associations, few studies have used quantitative community data to investigate the effects of ants on phyllosphere microbial communities. In the present study, we investigated the effects of ants on the phyllosphere fungal communities of Mallotus japonicus using high-throughput sequencing. Mallotus japonicus is a myrmecophilous plants that bears extrafloral nectaries, attracting several ant species, but does not provide specific ant species with nest sites like myrmecophytes do. We experimentally excluded ants with sticky resins from the target plants and collected leaf discs to extract fungal DNA. The ribosomal DNA internal transcribed spacer 1 (ITS1) regions of the phyllosphere fungi were amplified and sequenced to obtain fungal community data. Our results showed that the exclusion of ants changed the phyllosphere fungal community composition; however, the effect of ants on OTU richness was not clear. These results indicate that ants can change the community of phyllosphere fungi, even if the plant is not a myrmecophyte.
Collapse
Affiliation(s)
- Takafumi Mizuno
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Hirotoshi Sato
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| | - Takao Itioka
- Graduate School of Human and Environmental StudiesKyoto UniversityKyotoJapan
| |
Collapse
|
23
|
Andriienko V, Buczek M, Meier R, Srivathsan A, Łukasik P, Kolasa MR. Implementing high-throughput insect barcoding in microbiome studies: impact of non-destructive DNA extraction on microbiome reconstruction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.30.591865. [PMID: 38746196 PMCID: PMC11092579 DOI: 10.1101/2024.04.30.591865] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Background Symbiotic relationships with diverse microorganisms are crucial for many aspects of insect biology. However, while our understanding of insect taxonomic diversity and the distribution of insect species in natural communities is limited, we know much less about their microbiota. In the era of rapid biodiversity declines, as researchers increasingly turn towards DNA-based monitoring, developing and broadly implementing approaches for high-throughput and cost-effective characterization of both insect and insect-associated microbial diversity is essential. We need to verify whether approaches such as high-throughput barcoding, a powerful tool for identifying wild insects, would permit subsequent microbiota reconstruction in these specimens. Methods High-throughput barcoding ("megabarcoding") methods often rely on non-destructive approaches for obtaining template DNA for PCR amplification by leaching DNA out of insect specimens using alkaline buffers such as HotSHOT. This study investigated the impact of HotSHOT on microbial abundance estimates and the reconstructed bacterial community profiles. We addressed this question by comparing quantitative 16S rRNA amplicon sequencing data for HotSHOT-treated or untreated specimens of 16 insect species representing six orders and selected based on the expectation of limited variation among individuals. Results We find that in 13 species, the treatment significantly reduced microbial abundance estimates, corresponding to an estimated 15-fold decrease in amplifiable 16S rRNA template on average. On the other hand, HotSHOT pre-treatment had a limited effect on microbial community composition. The reconstructed presence of abundant bacteria with known significant effects was not affected. On the other hand, we observed changes in the presence of low-abundance microbes, those close to the reliable detection threshold. Alpha and beta diversity analyses showed compositional differences in only a few species. Conclusion Our results indicate that HotSHOT pre-treated specimens remain suitable for microbial community composition reconstruction, even if abundance may be hard to estimate. These results indicate that we can cost-effectively combine barcoding with the study of microbiota across wild insect communities. Thus, the voucher specimens obtained using megabarcoding studies targeted at characterizing insect communities can be used for microbiome characterizations. This can substantially aid in speeding up the accumulation of knowledge on the microbiomes of abundant and hyperdiverse insect species.
Collapse
Affiliation(s)
- Veronika Andriienko
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Institute of Zoology and Biomedical Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Kraków, Poland
| | - Mateusz Buczek
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | | | | | - Piotr Łukasik
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| | - Michał R Kolasa
- Institute of Environmental Sciences, Faculty of Biology, Jagiellonian University, Kraków, Poland
| |
Collapse
|
24
|
Bromfield JI, Zaugg J, Straw RC, Cathie J, Krueger A, Sinha D, Chandra J, Hugenholtz P, Frazer IH. Characterization of the skin microbiome in normal and cutaneous squamous cell carcinoma affected cats and dogs. mSphere 2024; 9:e0055523. [PMID: 38530017 PMCID: PMC11036808 DOI: 10.1128/msphere.00555-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Human cutaneous squamous cell carcinomas (SCCs) and actinic keratoses (AK) display microbial dysbiosis with an enrichment of staphylococcal species, which have been implicated in AK and SCC progression. SCCs are common in both felines and canines and are often diagnosed at late stages leading to high disease morbidity and mortality rates. Although recent studies support the involvement of the skin microbiome in AK and SCC progression in humans, there is no knowledge of this in companion animals. Here, we provide microbiome data for SCC in cats and dogs using culture-independent molecular profiling and show a significant decrease in microbial alpha diversity on SCC lesions compared to normal skin (P ≤ 0.05). Similar to human skin cancer, SCC samples had an elevated abundance of staphylococci relative to normal skin-50% (6/12) had >50% staphylococci, as did 16% (4/25) of perilesional samples. Analysis of Staphylococcus at the species level revealed an enrichment of the pathogenic species Staphylococcus felis in cat SCC samples, a higher prevalence of Staphylococcus pseudintermedius in dogs, and a higher abundance of Staphylococcus aureus compared to normal skin in both companion animals. Additionally, a comparison of previously published human SCC and perilesional samples against the present pet samples revealed that Staphylococcus was the most prevalent genera across human and companion animals for both sample types. Similarities between the microbial profile of human and cat/dog SCC lesions should facilitate future skin cancer research. IMPORTANCE The progression of precancerous actinic keratosis lesions (AK) to cutaneous squamous cell carcinoma (SCC) is poorly understood in humans and companion animals, despite causing a significant burden of disease. Recent studies have revealed that the microbiota may play a significant role in disease progression. Staphylococcus aureus has been found in high abundance on AK and SCC lesions, where it secretes DNA-damaging toxins, which could potentiate tumorigenesis. Currently, a suitable animal model to investigate this relationship is lacking. Thus, we examined the microbiome of cutaneous SCC in pets, revealing similarities to humans, with increased staphylococci and reduced commensals on SCC lesions and peri-lesional skin compared to normal skin. Two genera that were in abundance in SCC samples have also been found in human oral SCC lesions. These findings suggest the potential suitability of pets as a model for studying microbiome-related skin cancer progression.
Collapse
Affiliation(s)
- Jacoba I. Bromfield
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Julian Zaugg
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia
| | - Rodney C. Straw
- Brisbane Veterinary Specialist Centre and the Australian Animal Cancer Foundation, Albany Creek, Queensland, Australia
| | - Julia Cathie
- Brisbane Veterinary Specialist Centre and the Australian Animal Cancer Foundation, Albany Creek, Queensland, Australia
| | - Annika Krueger
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Debottam Sinha
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Janin Chandra
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| | - Philip Hugenholtz
- Australian Centre for Ecogenomics, University of Queensland, St Lucia, Queensland, Australia
| | - Ian H. Frazer
- Frazer Institute, Faculty of Medicine, The University of Queensland, Woolloongabba, Queensland, Australia
| |
Collapse
|
25
|
Dean CJ, Peña-Mosca F, Ray T, Wehri TJ, Sharpe K, Antunes, Jr. AM, Doster E, Fernandes L, Calles VF, Bauman C, Godden S, Heins B, Pinedo P, Machado VS, Caixeta LS, Noyes NR. Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives. Appl Environ Microbiol 2024; 90:e0223423. [PMID: 38497641 PMCID: PMC11022539 DOI: 10.1128/aem.02234-23] [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: 12/18/2023] [Accepted: 02/04/2024] [Indexed: 03/19/2024] Open
Abstract
The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26). IMPORTANCE Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.
Collapse
Affiliation(s)
- C. J. Dean
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - F. Peña-Mosca
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. Ray
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - T. J. Wehri
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - K. Sharpe
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - A. M. Antunes, Jr.
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - E. Doster
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - L. Fernandes
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - V. F. Calles
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - C. Bauman
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - S. Godden
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - B. Heins
- Department of Animal Science, University of Minnesota, St. Paul, Minnesota, USA
| | - P. Pinedo
- Department of Animal Science, Colorado State University, Fort Collins, Colorado, USA
| | - V. S. Machado
- Department of Veterinary Sciences, Texas Tech University, Lubbock, Texas, USA
| | - L. S. Caixeta
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| | - N. R. Noyes
- Department of Veterinary Population Medicine, University of Minnesota, St. Paul, Minnesota, USA
| |
Collapse
|
26
|
Bowron LA, Acosta N, Thornton CS, Carpentero J, Waddell BJM, Bharadwaj L, Ebbert K, Castañeda-Mogollón D, Conly JM, Rabin HR, Surette MG, Parkins MD. The airway microbiome of persons with cystic fibrosis correlates with acquisition and microbiological outcomes of incident Stenotrophomonas maltophilia infection. Front Microbiol 2024; 15:1353145. [PMID: 38690371 PMCID: PMC11059027 DOI: 10.3389/fmicb.2024.1353145] [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: 12/10/2023] [Accepted: 02/27/2024] [Indexed: 05/02/2024] Open
Abstract
Rationale Chronic infection with Stenotrophomonas maltophilia in persons with cystic fibrosis (pwCF) has been linked to an increased risk of pulmonary exacerbations and lung function decline. We sought to establish whether baseline sputum microbiome associates with risk of S. maltophilia incident infection and persistence in pwCF. Methods pwCF experiencing incident S. maltophilia infections attending the Calgary Adult CF Clinic from 2010-2018 were compared with S. maltophilia-negative sex, age (+/-2 years), and birth-cohort-matched controls. Infection outcomes were classified as persistent (when the pathogen was recovered in ≥50% of cultures in the subsequent year) or transient. We assessed microbial communities from prospectively biobanked sputum using V3-V4 16S ribosomal RNA (rRNA) gene sequencing, in the year preceding (Pre) (n = 57), at (At) (n = 22), and after (Post) (n = 31) incident infection. We verified relative abundance data using S. maltophilia-specific qPCR and 16S rRNA-targeted qPCR to assess bioburden. Strains were typed using pulse-field gel electrophoresis. Results Twenty-five pwCF with incident S. maltophilia (56% female, median 29 years, median FEV1 61%) with 33 total episodes were compared with 56 uninfected pwCF controls. Demographics and clinical characteristics were similar between cohorts. Among those with incident S. maltophilia infection, sputum communities did not cluster based on infection timeline (Pre, At, Post). Communities differed between the infection cohort and controls (n = 56) based on Shannon Diversity Index (SDI, p = 0.04) and clustered based on Aitchison distance (PERMANOVA, p = 0.01) prior to infection. At the time of incident S. maltophilia isolation, communities did not differ in SDI but clustered based on Aitchison distance (PERMANOVA, p = 0.03) in those that ultimately developed persistent infection versus those that were transient. S. maltophilia abundance within sputum was increased in samples from patients (Pre) relative to controls, measuring both relative (p = 0.004) and absolute (p = 0.001). Furthermore, S. maltophilia abundance was increased in sputum at incident infection in those who ultimately developed persistent infection relative to those with transient infection, measured relatively (p = 0.04) or absolute (p = 0.04), respectively. Conclusion Microbial community composition of CF sputum associates with S. maltophilia infection acquisition as well as infection outcome. Our study suggests sputum microbiome may serve as a surrogate for identifying infection risk and persistence risk.
Collapse
Affiliation(s)
- Lauren A. Bowron
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Nicole Acosta
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Christina S. Thornton
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Jennifer Carpentero
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Barbara-Jean M. Waddell
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Lalit Bharadwaj
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - Kirsten Ebbert
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Pediatrics, University of Calgary, Calgary, AB, Canada
| | - Daniel Castañeda-Mogollón
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
| | - John M. Conly
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | - Harvey R. Rabin
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| | | | - Michael D. Parkins
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, Calgary, AB, Canada
- Department of Medicine, University of Calgary, Calgary, AB, Canada
| |
Collapse
|
27
|
Gao J, Yang Y, Xiang X, Zheng H, Yi X, Wang F, Liang Z, Chen D, Shi W, Wang L, Wu D, Feng S, Huang Q, Li X, Shu W, Chen R, Zhong N, Wang Z. Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease. Respir Res 2024; 25:165. [PMID: 38622589 DOI: 10.1186/s12931-024-02805-2] [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: 09/20/2023] [Accepted: 04/04/2024] [Indexed: 04/17/2024] Open
Abstract
Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10-5), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10-8). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.
Collapse
Affiliation(s)
- Jingyuan Gao
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Yuqiong Yang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xiaopeng Xiang
- The Hong Kong Polytechnic University, Hong Kong, Hung Hom Kowloon, China
| | - Huimin Zheng
- Department of Obstetrics and Gynecology, The First People's Hospital of Foshan, Foshan, Guangdong Province, China
| | - Xinzhu Yi
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China
| | - Fengyan Wang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Zhenyu Liang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Dandan Chen
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Weijuan Shi
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Lingwei Wang
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Di Wu
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China
| | - Shengchuan Feng
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Qiaoyun Huang
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Xueping Li
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China
| | - Wensheng Shu
- Institute of Ecological Sciences, School of Life Sciences, South China Normal University, Guangzhou, Guangdong Province, China.
| | - Rongchang Chen
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
- Department of Pulmonary and Critical Care Medicine, Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital, The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology, Shenzhen, Guangdong Province, China.
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Disease, National Clinical Research Center for Respiratory Disease, National Center for Respiratory Medicine, Guangzhou Institute of Respiratory Health, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong Province, China.
| | - Zhang Wang
- Institute of Ecological Sciences, Biomedical Research Center, School of Life Sciences, State Key Laboratory of Respiratory Disease, South China Normal University, Guangzhou, Guangdong Province, China.
| |
Collapse
|
28
|
Zhang W, Gundel PE, Jáuregui R, Card SD, Mace WJ, Johnson RD, Bastías DA. The growth promotion in endophyte symbiotic plants does not penalise the resistance to herbivores and bacterial microbiota. PLANT, CELL & ENVIRONMENT 2024. [PMID: 38616528 DOI: 10.1111/pce.14912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/19/2024] [Accepted: 03/29/2024] [Indexed: 04/16/2024]
Abstract
A trade-off between growth and defence against biotic stresses is common in plants. Fungal endophytes of the genus Epichloë may relieve this trade-off in their host grasses since they can simultaneously induce plant growth and produce antiherbivore alkaloids that circumvent the need for host defence. The Epichloë ability to decouple the growth-defence trade-off was evaluated by subjecting ryegrass with and without Epichloë endophytes to an exogenous treatment with gibberellin (GA) followed by a challenge with Rhopalosiphum padi aphids. In agreement with the endophyte-mediated trade-off decoupling hypothesis, the GA-derived promotion of plant growth increased the susceptibility to aphids in endophyte-free plants but did not affect the insect resistance in endophyte-symbiotic plants. In line with the unaltered insect resistance, the GA treatment did not reduce the concentration of Epichloë-derived alkaloids. The Epichloë mycelial biomass was transiently increased by the GA treatment but at the expense of hyphal integrity. The response of the phyllosphere bacterial microbiota to both GA treatment and Epichloë was also evaluated. Only Epichloë, and not the GA treatment, altered the composition of the phyllosphere microbiota and the abundance of certain bacterial taxa. Our findings clearly demonstrate that Epichloë does indeed relieve the plant growth-defence trade-off.
Collapse
Affiliation(s)
- Wei Zhang
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Pedro E Gundel
- Centro de Ecología Integrativa, Instituto de Ciencias Biológicas, Universidad de Talca, Talca, Chile
| | - Ruy Jáuregui
- Animal Health Laboratory, Biosecurity New Zealand, Ministry for Primary Industries, Upper Hutt, New Zealand
| | - Stuart D Card
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Wade J Mace
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Richard D Johnson
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| | - Daniel A Bastías
- AgResearch Limited, Grasslands Research Centre, Palmerston North, New Zealand
| |
Collapse
|
29
|
Obregon-Gutierrez P, Bonillo-Lopez L, Correa-Fiz F, Sibila M, Segalés J, Kochanowski K, Aragon V. Gut-associated microbes are present and active in the pig nasal cavity. Sci Rep 2024; 14:8470. [PMID: 38605046 PMCID: PMC11009223 DOI: 10.1038/s41598-024-58681-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 04/02/2024] [Indexed: 04/13/2024] Open
Abstract
The nasal microbiota is a key contributor to animal health, and characterizing the nasal microbiota composition is an important step towards elucidating the role of its different members. Efforts to characterize the nasal microbiota composition of domestic pigs and other farm animals frequently report the presence of bacteria that are typically found in the gut, including many anaerobes from the Bacteroidales and Clostridiales orders. However, the in vivo role of these gut-microbiota associated taxa is currently unclear. Here, we tackled this issue by examining the prevalence, origin, and activity of these taxa in the nasal microbiota of piglets. First, analysis of the nasal microbiota of farm piglets sampled in this study, as well as various publicly available data sets, revealed that gut-microbiota associated taxa indeed constitute a substantial fraction of the pig nasal microbiota that is highly variable across individual animals. Second, comparison of herd-matched nasal and rectal samples at amplicon sequencing variant (ASV) level showed that these taxa are largely shared in the nasal and rectal microbiota, suggesting a common origin driven presumably by the transfer of fecal matter. Third, surgical sampling of the inner nasal tract showed that gut-microbiota associated taxa are found throughout the nasal cavity, indicating that these taxa do not stem from contaminations introduced during sampling with conventional nasal swabs. Finally, analysis of cDNA from the 16S rRNA gene in these nasal samples indicated that gut-microbiota associated taxa are indeed active in the pig nasal cavity. This study shows that gut-microbiota associated taxa are not only present, but also active, in the nasal cavity of domestic pigs, and paves the way for future efforts to elucidate the function of these taxa within the nasal microbiota.
Collapse
Affiliation(s)
- Pau Obregon-Gutierrez
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Laura Bonillo-Lopez
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Florencia Correa-Fiz
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Marina Sibila
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
| | - Joaquim Segalés
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain
- Departament de Sanitat i Anatomia Animals, Facultat de Veterinària, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain
| | - Karl Kochanowski
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain.
| | - Virginia Aragon
- Centre de Recerca en Sanitat Animal (CReSA), Unitat Mixta d'Investigació IRTA-UAB en Sanitat Animal, Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- IRTA, Programa de Sanitat Animal, Centre de Recerca en Sanitat Animal (CReSA), Campus de la Universitat Autònoma de Barcelona (UAB), Bellaterra, 08193, Barcelona, Spain.
- OIE Collaborating Centre for the Research and Control of Emerging and Re-Emerging Swine Diseases in Europe (IRTA-CReSA), Bellaterra, 08193, Barcelona, Spain.
| |
Collapse
|
30
|
Li M, Kopylova E, Mao J, Namkoong J, Sanders J, Wu J. Microbiome and lipidomic analysis reveal the interplay between skin bacteria and lipids in a cohort study. Front Microbiol 2024; 15:1383656. [PMID: 38666261 PMCID: PMC11043602 DOI: 10.3389/fmicb.2024.1383656] [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: 02/07/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
Human skin acts as a protective barrier between the body and the external environment. Skin microbiome and intercellular lipids in the stratum corneum (SC) are essential for maintaining skin barrier function. However, the interplay between skin bacteria and the lipids is not fully understood. In this study, we characterized the skin microbiome and SC lipid profiles from the forearm and face in a cohort of 57 healthy participants. 16S rRNA gene sequencing showed the skin microbial composition is significantly different between body locations and genders. Female forearm samples have the highest microbial diversity. The relative abundance of Staphylococcus hominis, Micrococcus luteus, Corynebacterium tuberculostearicum, Finegoldia magna, and Moraxellaceae sp. are significantly higher in the forearm than the face. The predictive functional analysis of 16S rRNA gene sequencing by Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) and ANCOM-BC showed different bacterial metabolic pathway profiles between body locations or genders, and identified 271 differential pathways, including arginine and polyamine biosynthesis, chorismate biosynthesis pathways, which are more abundant in the female forearm, and sulfur oxidation pathway, which is more abundant in the male face. The SC lipid profiles differ between the body locations as well. Total free fatty acids (FFA), cholesterol sulfate and sphingosine are more abundant in the face. Dihydro-/6-hydroxy/phyto-ceramides are more abundant in the forearm. The correlation analysis of 16S rRNA gene sequencing and lipids revealed novel interplay between the bacteria and skin lipids. Shannon entropy and S. hominis negatively correlated with FFA, cholesterol sulfate and sphingosine; while positively correlated with dihydro-/6-hydroxy/phyto-ceramides. The correlation of predictive pathway profiles and lipids identified pathways involved in amino acids metabolism, carbohydrates degradation, aromatic compounds metabolism and fatty acid degradation metabolism are positively correlated with dihydro-/6-hydroxy/phyto-ceramides and negatively correlated with FFA, cholesterol sulfate and sphingosine. This study provides insights on the potential correlation between skin microbiome and lipids.
Collapse
Affiliation(s)
- Min Li
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | | | - Junhong Mao
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | - Jin Namkoong
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| | - Jon Sanders
- Clarity Genomics, San Diego, CA, United States
| | - Joanna Wu
- Colgate-Palmolive Company, Global Technology Center, Piscataway, NJ, United States
| |
Collapse
|
31
|
Thøgersen MS, Zervas A, Stougaard P, Ellegaard-Jensen L. Investigating eukaryotic and prokaryotic diversity and functional potential in the cold and alkaline ikaite columns in Greenland. Front Microbiol 2024; 15:1358787. [PMID: 38655082 PMCID: PMC11035741 DOI: 10.3389/fmicb.2024.1358787] [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: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 04/26/2024] Open
Abstract
The ikaite columns in the Ikka Fjord, SW Greenland, represent a permanently cold and alkaline environment known to contain a rich bacterial diversity. 16S and 18S rRNA gene amplicon and metagenomic sequencing was used to investigate the microbial diversity in the columns and for the first time, the eukaryotic and archaeal diversity in ikaite columns were analyzed. The results showed a rich prokaryotic diversity that varied across columns as well as within each column. Seven different archaeal phyla were documented in multiple locations inside the columns. The columns also contained a rich eukaryotic diversity with 27 phyla representing microalgae, protists, fungi, and small animals. Based on metagenomic sequencing, 25 high-quality MAGs were assembled and analyzed for the presence of genes involved in cycling of nitrogen, sulfur, and phosphorous as well as genes encoding carbohydrate-active enzymes (CAZymes), showing a potentially very bioactive microbial community.
Collapse
|
32
|
Zhao Y, Liao Y, Xu G, Wang Y. Endometrial microbiota alteration in female patients with endometrial polyps based on 16S rRNA gene sequencing analysis. Front Cell Infect Microbiol 2024; 14:1351329. [PMID: 38655283 PMCID: PMC11035718 DOI: 10.3389/fcimb.2024.1351329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 03/11/2024] [Indexed: 04/26/2024] Open
Abstract
Introduction The potential role of the endometrial microbiota in the pathogenesis of endometrial polyps (EPs) warrants further investigation, given the current landscape of limited and inconclusive research findings. We aimed to explore the microecological characteristics of the uterine cavity in patients with EPs and investigate the potential of endometrial microbiota species as novel biomarkers for identifying EPs. Methods Endometrial samples were collected from 225 patients who underwent hysteroscopies, of whom 167 had EPs, whereas 58 had non- hyperproliferative endometrium status. The endometrial microbiota was assessed using 16S rRNA gene sequencing. We characterized the endometrial microbiota and identified microbial biomarkers for predicting EPs. Results The endometrial microbial diversity and composition were significantly different between the EP and control groups. Predictive functional analyses of the endometrial microbiota demonstrated significant alterations in pathways involved in sphingolipid metabolism, steroid hormone biosynthesis, and apoptosis between the two groups. Moreover, a classification model based on endometrial microbial ASV-based biomarkers along with the presence of abnormal uterine bleeding symptoms achieved powerful classification potential in identifying EPs in both the discovery and validation cohorts. Conclusion Our study indicates a potential association between altered endometrial microbiota and EPs. Endometrial microbiota-based biomarkers may prove valuable for the diagnosis of EPs. Clinical trial registration Chinese Clinical Trial Registry (ChiCTR2100052746).
Collapse
Affiliation(s)
- Yu Zhao
- Department of Ambulatory Surgery, Women’s Hospital School of Medicine Zhejiang University, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yun Liao
- Department of Ambulatory Surgery, Women’s Hospital School of Medicine Zhejiang University, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
- Zhejiang Provincial Key Laboratory of Precision Diagnosis and Therapy for Major Gynecological Diseases, Women’s Hospital School of Medicine Zhejiang University, Hangzhou, China
| | - Gufeng Xu
- Department of Ambulatory Surgery, Women’s Hospital School of Medicine Zhejiang University, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| | - Yue Wang
- Department of Ambulatory Surgery, Women’s Hospital School of Medicine Zhejiang University, Hangzhou, China
- Zhejiang Provincial Clinical Research Center for Obstetrics and Gynecology, Hangzhou, China
| |
Collapse
|
33
|
Rodríguez-García C, Abad-Rodríguez I, López-Báez J, Cabrera-Castro R. A life in the surf zone: Age and feeding habits of the pompano (Trachinotus ovatus, Linnaeus, 1758) on the beaches of the Gulf of Cádiz (south-west Iberian Peninsula). JOURNAL OF FISH BIOLOGY 2024; 104:1152-1164. [PMID: 38230436 DOI: 10.1111/jfb.15661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/18/2024]
Abstract
Surf zones are crucial habitats for many fish species, where they spend the initial stages of their lives, finding food and shelter. One such species is the pompano (Trachinotus ovatus). The aim of this study was to examine the age and diet of the pompano within the surf zone, along with any potential variations in the environment. The average size of the specimens was 10.61 ± 4.91 cm. The length-weight relationship was total weight (TW) = 0.0136*total length (TL)2.8512 (parameter a: 95% C.I.: 0.0130-0.0142 and parameter b: 95% C.I.: 2.8318-2.8705). The most abundant age classes were 0+ and 1+, making up 97% of the captured specimens, with significant differences in the abundance of age classes depending on the time of the day and season. The pompano primarily fed on clupeiforms, copepods, and mysids, with significant variations in diet based on the time of the day, season, and size of the specimens. This study contributes new information about the use of the surf zone by T. ovatus in its early years of life, underscoring the importance of these areas and their role as an additional ecosystem service.
Collapse
Affiliation(s)
- Carlos Rodríguez-García
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus Río San Pedro, Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEIMAR), Puerto Real, Spain
| | - Isabel Abad-Rodríguez
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus Río San Pedro, Universidad de Cádiz, Puerto Real, Spain
| | - Jesús López-Báez
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus Río San Pedro, Universidad de Cádiz, Puerto Real, Spain
| | - Remedios Cabrera-Castro
- Departamento de Biología, Facultad de Ciencias del Mar y Ambientales, Campus Río San Pedro, Universidad de Cádiz, Puerto Real, Spain
- Instituto Universitario de Investigación Marina (INMAR), Campus de Excelencia Internacional del Mar (CEIMAR), Puerto Real, Spain
| |
Collapse
|
34
|
Bonfim M, López DP, Repetto MF, Freestone AL. Speed and degree of functional and compositional recovery varies with latitude and community age. Ecology 2024; 105:e4259. [PMID: 38404022 DOI: 10.1002/ecy.4259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/29/2023] [Accepted: 12/21/2023] [Indexed: 02/27/2024]
Abstract
Rates at which a community recovers after disturbance, or its resilience, can be accelerated by increased net primary productivity and recolonization dynamics such as recruitment. These mechanisms can vary across biogeographic gradients, such as latitude, suggesting that biogeography is likely important to predicting resilience. To test whether community resilience, informed by functional and compositional recovery, hinges on geographic location, we employed a standardized replicated experiment on marine invertebrate communities across four regions from the tropics to the subarctic zone. Communities assembled naturally on standardized substrate while experiencing distinct levels of biomass removal (no removal, low disturbance, and high disturbance), which opened space for new colonizers, thereby providing a pulse of limited resource to these communities. We then quantified functional (space occupancy and biomass) and compositional recovery from these repeated pulse disturbances across two community assembly timescales (early and late at 3 and 12 months, respectively). We documented latitudinal variation in resilience across 47° latitude, where speed of functional recovery was higher toward lower latitudes yet incomplete at late assembly in the tropics and subtropics. The degree of functional recovery did not coincide with compositional recovery, and regional differences in recruitment and growth likely contributed to functional recovery in these communities. While biogeographic variation in community resilience has been predicted, our results are among the first to examine functional and compositional recovery from disturbance in a single large-scale standardized experiment.
Collapse
Affiliation(s)
- Mariana Bonfim
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
| | - Diana P López
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Smithsonian Tropical Research Institute, Ancon, Panama
| | - Michele F Repetto
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| | - Amy L Freestone
- Department of Biology, Temple University, Philadelphia, Pennsylvania, USA
- Smithsonian Tropical Research Institute, Ancon, Panama
- Smithsonian Environmental Research Center, Edgewater, Maryland, USA
| |
Collapse
|
35
|
Mucsi M, Borsodi AK, Megyes M, Szili-Kovács T. Response of the metabolic activity and taxonomic composition of bacterial communities to mosaically varying soil salinity and alkalinity. Sci Rep 2024; 14:7460. [PMID: 38553497 PMCID: PMC10980690 DOI: 10.1038/s41598-024-57430-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 03/18/2024] [Indexed: 04/02/2024] Open
Abstract
Soil salinity and sodicity is a worldwide problem that affects the composition and activity of bacterial communities and results from elevated salt and sodium contents. Depending on the degree of environmental pressure and the combined effect of other factors, haloalkalitolerant and haloalkaliphilic bacterial communities will be selected. These bacteria play a potential role in the maintenance and restoration of salt-affected soils; however, until recently, only a limited number of studies have simultaneously studied the bacterial diversity and activity of saline-sodic soils. Soil samples were collected to analyse and compare the taxonomic composition and metabolic activity of bacteria from four distinct natural plant communities at three soil depths corresponding to a salinity‒sodicity gradient. Bacterial diversity was detected using 16S rRNA gene Illumina MiSeq amplicon sequencing. Community-level physiological profiles (CLPPs) were analysed using the MicroResp™ method. The genus-level bacterial composition and CLPPs differed significantly in soils with different alkaline vegetation. The surface soil samples also significantly differed from the intermediate and deep soil samples. The results showed that the pH, salt content, and Na+ content of the soils were the main edaphic factors influencing both bacterial diversity and activity. With salinity and pH, the proportion of the phylum Gemmatimonadota increased, while the proportions of Actinobacteriota and Acidobacteriota decreased.
Collapse
Affiliation(s)
- Márton Mucsi
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15, Budapest, 1022, Hungary
- Doctoral School of Environmental Sciences, ELTE Eötvös Loránd University, Pázmány P. sétány 1/AC, Budapest, 1117, Hungary
| | - Andrea K Borsodi
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, Budapest, 1117, Hungary.
- Institute of Aquatic Ecology, HUN-REN Centre for Ecological Research, Karolina út 29, Budapest, 1113, Hungary.
| | - Melinda Megyes
- Doctoral School of Environmental Sciences, ELTE Eötvös Loránd University, Pázmány P. sétány 1/AC, Budapest, 1117, Hungary
- Department of Microbiology, ELTE Eötvös Loránd University, Pázmány P. sétány 1/C, Budapest, 1117, Hungary
| | - Tibor Szili-Kovács
- Institute for Soil Sciences, HUN-REN Centre for Agricultural Research, Herman Ottó út 15, Budapest, 1022, Hungary.
| |
Collapse
|
36
|
He M, Zhao N, Satten GA. MIDASim: a fast and simple simulator for realistic microbiome data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.03.23.533996. [PMID: 36993431 PMCID: PMC10055388 DOI: 10.1101/2023.03.23.533996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
Background Advances in sequencing technology has led to the discovery of associations between the human microbiota and many diseases, conditions, and traits. With the increasing availability of microbiome data, many statistical methods have been developed for studying these associations. The growing number of newly developed methods highlights the need for simple, rapid, and reliable methods to simulate realistic microbiome data, which is essential for validating and evaluating the performance of these methods. However, generating realistic microbiome data is challenging due to the complex nature of microbiome data, which feature correlation between taxa, sparsity, overdispersion, and compositionality. Current methods for simulating microbiome data are deficient in their ability to capture these important features of microbiome data, or can require exorbitant computational time. Methods We develop MIDASim ( MI crobiome DA ta Sim ulator), a fast and simple approach for simulating realistic microbiome data that reproduces the distributional and correlation structure of a template microbiome dataset. MIDASim is a two-step approach. The first step generates correlated binary indicators that represent the presence-absence status of all taxa, and the second step generates relative abundances and counts for the taxa that are considered to be present in step 1, utilizing a Gaussian copula to account for the taxon-taxon correlations. In the second step, MIDASim can operate in both a nonparametric and parametric mode. In the nonparametric mode, the Gaussian copula uses the empirical distribution of relative abundances for the marginal distributions. In the parametric mode, an inverse generalized gamma distribution is used in place of the empirical distribution. Results We demonstrate improved performance of MIDASim relative to other existing methods using gut and vaginal data. MIDASim showed superior performance by PER-MANOVA and in terms of alpha diversity and beta dispersion in either parametric or nonparametric mode. We also show how MIDASim in parametric mode can be used to assess the performance of methods for finding differentially abundant taxa in a compositional model. Conclusions MIDASim is easy to implement, flexible and suitable for most microbiome data simulation situations. MIDASim has three major advantages. First, MIDASim performs better in reproducing the distributional features of real data compared to other methods at both presence-absence level and relative-abundance level. MIDASim-simulated data are more similar to the template data than competing methods, as quantified using a variety of measures. Second, MIDASim makes few distributional assumptions for the relative abundances, and thus can easily accommodate complex distributional features in real data. Third, MIDASim is computationally efficient and can be used to simulate large microbiome datasets.
Collapse
|
37
|
Pei L, Ye S, Xie L, Zhou P, He L, Yang S, Ding X, Yuan H, Dai T, Laws EA. Differential effects of warming on the complexity and stability of the microbial network in Phragmites australis and Spartina alterniflora wetlands in Yancheng, Jiangsu Province, China. Front Microbiol 2024; 15:1347821. [PMID: 38601935 PMCID: PMC11004437 DOI: 10.3389/fmicb.2024.1347821] [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: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
The impact of climate warming on soil microbial communities can significantly influence the global carbon cycle. Coastal wetlands, in particular, are susceptible to changes in soil microbial community structure due to climate warming and the presence of invasive plant species. However, there is limited knowledge about how native and invasive plant wetland soil microbes differ in their response to warming. In this study, we investigated the temporal dynamics of soil microbes (prokaryotes and fungi) under experimental warming in two coastal wetlands dominated by native Phragmites australis (P. australis) and invasive Spartina alterniflora (S. alterniflora). Our research indicated that short-term warming had minimal effects on microbial abundance, diversity, and composition. However, it did accelerate the succession of soil microbial communities, with potentially greater impacts on fungi than prokaryotes. Furthermore, in the S. alterniflora wetland, experimental warming notably increased the complexity and connectivity of the microbial networks. While in the P. australis wetland, it decreased these factors. Analysis of robustness showed that experimental warming stabilized the co-occurrence network of the microbial community in the P. australis wetland, but destabilized it in the S. alterniflora wetland. Additionally, the functional prediction analysis using the Faprotax and FunGuild databases revealed that the S. alterniflora wetland had a higher proportion of saprotrophic fungi and prokaryotic OTUs involved in carbon degradation (p < 0.05). With warming treatments, there was an increasing trend in the proportion of prokaryotic OTUs involved in carbon degradation, particularly in the S. alterniflora wetland. Therefore, it is crucial to protect native P. australis wetlands from S. alterniflora invasion to mitigate carbon emissions and preserve the health of coastal wetland ecosystems under future climate warming in China.
Collapse
Affiliation(s)
- Lixin Pei
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Siyuan Ye
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Liujuan Xie
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Pan Zhou
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Lei He
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Shixiong Yang
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Xigui Ding
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Hongming Yuan
- Qingdao Institute of Marine Geology, China Geologic Survey, Qingdao, China
- Laboratory for Marine Geology, Qingdao Marine Science and Technology Center, Qingdao, China
| | - Tianjiao Dai
- School of Water Resources and Environment, China University of Geosciences (Beijing), Beijing, China
| | - Edward A. Laws
- Department of Environmental Sciences, College of the Coast and Environment, Louisiana State University, Baton Rouge, LA, United States
| |
Collapse
|
38
|
Guaschino M, Garello M, Nari L, Zhimo YV, Droby S, Spadaro D. Soil, rhizosphere, and root microbiome in kiwifruit vine decline, an emerging multifactorial disease. Front Microbiol 2024; 15:1330865. [PMID: 38577679 PMCID: PMC10991698 DOI: 10.3389/fmicb.2024.1330865] [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: 10/31/2023] [Accepted: 02/14/2024] [Indexed: 04/06/2024] Open
Abstract
Kiwifruit vine decline syndrome (KVDS) is characterized by severe root system impairment, which leads to irreversible wilting of the canopy. Plants usually collapse rapidly from the appearance of the first aboveground symptoms, without recovery even in the following seasons. The syndrome has been negatively impacting kiwifruit yield in different areas of Italy, the main producing European country, since its first outbreak in 2012. To date, a unique, common causal factor has yet to be found, and the syndrome is referred to as multifactorial. In this article, we investigated the whole biotic community (fungi, bacteria, and oomycetes) associated with the development of KVDS in three different belowground matrices/compartments (soil, rhizosphere, and root). Sampling was performed at both healthy and affected sites located in the main kiwifruit-producing area of Northwestern Italy. To address the multifactorial nature of the syndrome and to investigate the potential roles of abiotic factors in shaping these communities, a physicochemical analysis of soils was also performed. This study investigates the associations among taxonomic groups composing the microbiome and also between biotic and abiotic factors. Dysbiosis was considered as a driving event in shaping KVDS microbial communities. The results obtained from this study highlight the role of the oomycete genus Phytopythium, which resulted predominantly in the oomycete community composition of diseased matrices, though it was also present in healthy ones. Both bacterial and fungal communities resulted in a high richness of genera and were highly correlated to the sampling site and matrix, underlining the importance of multiple location sampling both geographically and spatially. The rhizosphere community associated with KVDS was driven by a dysbiotic process. In addition, analysis of the association network in the diseased rhizosphere revealed the presence of potential cross-kingdom competition for plant-derived carbon between saprobes, oomycetes, and bacteria.
Collapse
Affiliation(s)
- Micol Guaschino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | - Marco Garello
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| | | | - Yeka V. Zhimo
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Samir Droby
- Department of Postharvest Science, ARO, The Volcani Center, Rishon LeZion, Israel
| | - Davide Spadaro
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Grugliasco, Italy
- Interdepartmental Centre for Innovation in Agro-environmental Sector – AGROINNOVA, University of Turin, Grugliasco, Italy
| |
Collapse
|
39
|
Türtscher J, Jambura PL, Villalobos-Segura E, López-Romero FA, Underwood CJ, Thies D, Lauer B, Lauer R, Kriwet J. Rostral and body shape analyses reveal cryptic diversity of Late Jurassic batomorphs (Chondrichthyes, Elasmobranchii) from Europe. PAPERS IN PALAEONTOLOGY 2024; 10:e1552. [PMID: 38799546 PMCID: PMC7615989 DOI: 10.1002/spp2.1552] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 01/08/2024] [Indexed: 05/29/2024]
Abstract
The fossil record of chondrichthyans (chimaeras, sharks, rays and skates) consists largely of isolated teeth, with holomorphic specimens being extraordinary exceptions. However, numerous of these more or less completely preserved specimens are known from several Upper Jurassic deposits of Europe, enabling detailed analysis of their morphology. Batomorphs (rays and skates) resembling modern guitarfishes and wedgefishes (Rhinopristiformes) are among the most common Jurassic chondrichthyans found, but they have been only sporadically studied up to now, resulting in large knowledge gaps concerning their taxonomy and phylogeny. Here, we present the most detailed revision of Late Jurassic holomorphic batomorphs to date, quantitatively analysing body proportions of specimens from Germany (Solnhofen Archipelago), France (Cerin) and the UK (Kimmeridge), using both geometric and traditional morphometrics. Furthermore, we identify qualitative morphological characters for species discrimination, to clarify the taxonomic identity and diversity of Late Jurassic batomorphs based on holomorphic specimens. Our results support the validity of Belemnobatis sismondae, Kimmerobatis etchesi and Spathobatis bugesiacus, as well as that of the previously doubtful Asterodermus platypterus. Moreover, we describe Aellopobatis bavarica, a new taxon, which has hitherto been considered to be a large-sized morphotype of Spathobatis bugesiacus. Our results highlight that the diversity of holomorphic batomorphs during the Late Jurassic was greater than previously thought, and suggest that this group was already well-established and diverse by this time. This study thus provides vital information about the evolutionary history of Late Jurassic batomorphs and has direct implications for batomorph species that are based on isolated teeth only.
Collapse
Affiliation(s)
- Julia Türtscher
- Department of Palaeontology, Faculty of Earth Sciences, Geography & Astronomy, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology & Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Patrick L. Jambura
- Department of Palaeontology, Faculty of Earth Sciences, Geography & Astronomy, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology & Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Eduardo Villalobos-Segura
- Department of Palaeontology, Faculty of Earth Sciences, Geography & Astronomy, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | - Faviel A. López-Romero
- Department of Palaeontology, Faculty of Earth Sciences, Geography & Astronomy, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | | | - Detlev Thies
- Zentrale Einrichtung für Weiterbildung, Leibniz Universität Hannover, Schloßwender Straße 5+7, 30159 Hannover, Germany
| | - Bruce Lauer
- Lauer Foundation for Paleontology, Science & Education, Wheaton, ILs, USA
| | - René Lauer
- Lauer Foundation for Paleontology, Science & Education, Wheaton, ILs, USA
| | - Jürgen Kriwet
- Department of Palaeontology, Faculty of Earth Sciences, Geography & Astronomy, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
- Vienna Doctoral School of Ecology & Evolution (VDSEE), University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| |
Collapse
|
40
|
Capadona J, Hoeferlin G, Grabinski S, Druschel L, Duncan J, Burkhart G, Weagraff G, Lee A, Hong C, Bambroo M, Olivares H, Bajwa T, Memberg W, Sweet J, Hamedani HA, Acharya A, Hernandez-Reynoso A, Donskey C, Jaskiw G, Chan R, Ajiboye A, von Recum H, Zhang L. Bacteria Invade the Brain Following Sterile Intracortical Microelectrode Implantation. RESEARCH SQUARE 2024:rs.3.rs-3980065. [PMID: 38496527 PMCID: PMC10942555 DOI: 10.21203/rs.3.rs-3980065/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Brain-machine interface performance is largely affected by the neuroinflammatory responses resulting in large part from blood-brain barrier (BBB) damage following intracortical microelectrode implantation. Recent findings strongly suggest that certain gut bacterial constituents penetrate the BBB and are resident in various brain regions of rodents and humans, both in health and disease. Therefore, we hypothesized that damage to the BBB caused by microelectrode implantation could amplify dysregulation of the microbiome-gut-brain axis. Here, we report that bacteria, including those commonly found in the gut, enter the brain following intracortical microelectrode implantation in mice implanted with single-shank silicon microelectrodes. Systemic antibiotic treatment of mice implanted with microelectrodes to suppress bacteria resulted in differential expression of bacteria in the brain tissue and a reduced acute inflammatory response compared to untreated controls, correlating with temporary improvements in microelectrode recording performance. Long-term antibiotic treatment resulted in worsening microelectrode recording performance and dysregulation of neurodegenerative pathways. Fecal microbiome composition was similar between implanted mice and an implanted human, suggesting translational findings. However, a significant portion of invading bacteria was not resident in the brain or gut. Together, the current study established a paradigm-shifting mechanism that may contribute to chronic intracortical microelectrode recording performance and affect overall brain health following intracortical microelectrode implantation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ricky Chan
- Institute for Computational Biology, Case Western Reserve University
| | | | | | | |
Collapse
|
41
|
Schrader L, Trautner J, Tebbe CC. Identifying environmental factors affecting the microbial community composition on outdoor structural timber. Appl Microbiol Biotechnol 2024; 108:254. [PMID: 38446240 PMCID: PMC10917859 DOI: 10.1007/s00253-024-13089-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/19/2024] [Accepted: 02/25/2024] [Indexed: 03/07/2024]
Abstract
Timber wood is a building material with many positive properties. However, its susceptibility to microbial degradation is a major challenge for outdoor usage. Although many wood-degrading fungal species are known, knowledge on their prevalence and diversity causing damage to exterior structural timber is still limited. Here, we sampled 46 decaying pieces of wood from outdoor constructions in the area of Hamburg, Germany; extracted their DNA; and investigated their microbial community composition by PCR amplicon sequencing of the fungal ITS2 region and partial bacterial 16S rRNA genes. In order to establish a link between the microbial community structure and environmental factors, we analysed the influence of wood species, its C and N contents, the effect of wood-soil contact, and the importance of its immediate environment (city, forest, meadow, park, respectively). We found that fungal and bacterial community composition colonising exterior timber was similar to fungi commonly found in forest deadwood. Of all basidiomycetous sequences retrieved, some, indicative for Perenniporia meridionalis, Dacrymyces capitatus, and Dacrymyces stillatus, were more frequently associated with severe wood damage. Whilst the most important environmental factor shaping fungal and bacterial community composition was the wood species, the immediate environment was important for fungal species whilst, for the occurrence of bacterial taxa, soil contact had a high impact. No influence was tangible for variation of the C or N content. In conclusion, our study demonstrates that wood colonising fungal and bacterial communities are equally responsive in their composition to wood species, but respond differently to environmental factors. KEY POINTS: • Perenniporia meridionalis and Dacrymyces are frequently associated with wood damage • Fungal community composition on timber is affected by its surrounding environment • Bacterial community composition on structural timber is affected by soil contact.
Collapse
Affiliation(s)
- Lauritz Schrader
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Jochen Trautner
- Thünen Institute of Wood Research, Leuschnerstraße 91, 21031, Hamburg, Germany
| | - Christoph C Tebbe
- Thünen Institute of Biodiversity, Bundesallee 65, 38116, Brunswick, Germany.
| |
Collapse
|
42
|
VanderRoest JP, Fowler JA, Rhoades CC, Roth HK, Broeckling CD, Fegel TS, McKenna AM, Bechtold EK, Boot CM, Wilkins MJ, Borch T. Fire Impacts on the Soil Metabolome and Organic Matter Biodegradability. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024; 58:4167-4180. [PMID: 38385432 DOI: 10.1021/acs.est.3c09797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Global wildfire activity has increased since the 1970s and is projected to intensify throughout the 21st century. Wildfires change the composition and biodegradability of soil organic matter (SOM) which contains nutrients that fuel microbial metabolism. Though persistent forms of SOM often increase postfire, the response of more biodegradable SOM remains unclear. Here we simulated severe wildfires through a controlled "pyrocosm" approach to identify biodegradable sources of SOM and characterize the soil metabolome immediately postfire. Using microbial amplicon (16S/ITS) sequencing and gas chromatography-mass spectrometry, heterotrophic microbes (Actinobacteria, Firmicutes, and Protobacteria) and specific metabolites (glycine, protocatechuate, citric cycle intermediates) were enriched in burned soils, indicating that burned soils contain a variety of substrates that support microbial metabolism. Molecular formulas assigned by 21 T Fourier transform ion cyclotron resonance mass spectrometry showed that SOM in burned soil was lower in molecular weight and featured 20 to 43% more nitrogen-containing molecular formulas than unburned soil. We also measured higher water extractable organic carbon concentrations and higher CO2 efflux in burned soils. The observed enrichment of biodegradable SOM and microbial heterotrophs demonstrates the resilience of these soils to severe burning, providing important implications for postfire soil microbial and plant recolonization and ecosystem recovery.
Collapse
Affiliation(s)
- Jacob P VanderRoest
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Julie A Fowler
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Charles C Rhoades
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Holly K Roth
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Corey D Broeckling
- Bioanalysis and Omics Center, Analytical Resources Core, Colorado State University, Fort Collins, 80521, United States
| | - Timothy S Fegel
- Rocky Mountain Research Station, U.S. Forest Service, Fort Collins, Colorado 80526, United States
| | - Amy M McKenna
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Dr., Tallahassee, Florida 32310, United States
| | - Emily K Bechtold
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Claudia M Boot
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Michael J Wilkins
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| | - Thomas Borch
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80521, United States
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado 80521, United States
| |
Collapse
|
43
|
Leigh RJ, Corrigan A, Murphy RA, Taylor-Pickard J, Moran CA, Walsh F. Yeast mannan rich fraction positively influences microbiome uniformity, productivity associated taxa, and lay performance. Anim Microbiome 2024; 6:9. [PMID: 38438939 PMCID: PMC10913240 DOI: 10.1186/s42523-024-00295-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 02/11/2024] [Indexed: 03/06/2024] Open
Abstract
BACKGROUND Alternatives to antibiotic as growth promoters in agriculture, such as supplemental prebiotics, are required to maintain healthy and high performing animals without directly contributing to antimicrobial resistance bioburden. While the gut microbiota of broiler hens has been well established and successfully correlated to performance, to our knowledge, a study has yet to be completed on the effect of prebiotic supplementation on correlating the mature laying hen productivity and microbiota. This study focused on establishing the impact of a yeast derived prebiotic, mannan rich fraction (MRF), on the cecal microbiota of late laying hens. This study benefitted from large sample sizes so intra- and intergroup variation effects could be statistically accounted for. RESULTS Taxonomic richness was significantly greater at all taxonomic ranks and taxonomic evenness was significantly lower for all taxonomic ranks in MRF-supplemented birds (P < 0.005). Use of principal coordinate analyses and principal component analyses found significant variation between treatment groups. When assessed for compositional uniformity (an indicator of flock health), microbiota in MRF-supplemented birds was more uniform than control birds at the species level. From a food safety and animal welfare perspective, Campylobacter jejuni was significantly lower in abundance in MRF-supplemented birds. In this study, species associated with high weight gain (an anticorrelator of performance in laying hens) were significantly lower in abundance in laying hens while health-correlated butyrate and propionate producing species were significantly greater in abundance in MRF-supplemented birds. CONCLUSIONS The use of prebiotics may be a key factor in controlling the microbiota balance limiting agri-food chain pathogen persistence and in promoting uniformity. In previous studies, increased α- and β-diversity indices were determinants of pathogen mitigation and performance. MRF-supplemented birds in this study established greater α- and β-diversity indices in post-peak laying hens, greater compositional uniformity across samples, a lower pathogenic bioburden and a greater abundance of correlators of performance.
Collapse
Affiliation(s)
- Robert J Leigh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| | | | | | | | - Colm A Moran
- Alltech SARL, Rue Charles Amand, 14500, Vire, France
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare, Ireland.
| |
Collapse
|
44
|
Rudzki EN, Antonson ND, Jones TM, Schelsky WM, Trevelline BK, Hauber ME, Kohl KD. Host avian species and environmental conditions influence the microbial ecology of brood parasitic brown-headed cowbird nestlings: What rules the roost? Mol Ecol 2024; 33:e17289. [PMID: 38327124 DOI: 10.1111/mec.17289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/09/2024]
Abstract
The role of species interactions, as well as genetic and environmental factors, all likely contribute to the composition and structure of the gut microbiome; however, disentangling these independent factors under field conditions represents a challenge for a functional understanding of gut microbial ecology. Avian brood parasites provide unique opportunities to investigate these questions, as brood parasitism results in parasite and host nestlings being raised in the same nest, by the same parents. Here we utilized obligate brood parasite brown-headed cowbird nestlings (BHCO; Molothrus ater) raised by several different host passerine species to better understand, via 16S rRNA sequencing, the microbial ecology of brood parasitism. First, we compared faecal microbial communities of prothonotary warbler nestlings (PROW; Protonotaria citrea) that were either parasitized or non-parasitized by BHCO and communities among BHCO nestlings from PROW nests. We found that parasitism by BHCO significantly altered both the community membership and community structure of the PROW nestling microbiota, perhaps due to the stressful nest environment generated by brood parasitism. In a second dataset, we compared faecal microbiotas from BHCO nestlings raised by six different host passerine species. Here, we found that the microbiota of BHCO nestlings was significantly influenced by the parental host species and the presence of an inter-specific nestmate. Thus, early rearing environment is important in determining the microbiota of brood parasite nestlings and their companion nestlings. Future work may aim to understand the functional effects of this microbiota variability on nestling performance and fitness.
Collapse
Affiliation(s)
- Elizabeth N Rudzki
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Nicholas D Antonson
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Todd M Jones
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
| | - Wendy M Schelsky
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Prairie Research Institute, Illinois Natural History Survey, University of Illinois, Champaign, Illinois, USA
| | - Brian K Trevelline
- Cornell Lab of Ornithology, Cornell University, Ithaca, New York, USA
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, New York, USA
| | - Mark E Hauber
- Department of Evolution, Ecology, and Behavior, School of Integrative Biology, College of Liberal Arts & Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Champaign, Illinois, USA
- Advanced Science Research Center and Program in Psychology, Graduate Center, City University of New York, New York, New York, USA
| | - Kevin D Kohl
- Department of Biological Sciences, Dietrich School of Arts and Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| |
Collapse
|
45
|
Mintrone C, Rindi L, Benedetti-Cecchi L. Stabilizing effects of spatially heterogeneous disturbance via reduced spatial synchrony on a rocky shore community. Ecology 2024; 105:e4246. [PMID: 38286517 DOI: 10.1002/ecy.4246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 10/24/2023] [Accepted: 12/05/2023] [Indexed: 01/31/2024]
Abstract
Understanding how synchronous species fluctuations affect community stability is a main research topic in ecology. Yet experimental studies evaluating how changes in disturbance regimes affect the synchrony and stability of populations and communities remain rare. We hypothesized that spatially heterogeneous disturbances of moderate intensity would promote metacommunity stability by decreasing the spatial synchrony of species fluctuations. To test this hypothesis, we exposed rocky shore communities of algae and invertebrates to homogeneous and gradient-like spatial patterns of disturbance at two levels of intensity for 4 years and used synchrony networks to characterize community responses to these disturbances. The gradient-like disturbance at low intensity enhanced spatial β diversity compared to the other treatments and produced the most heterogeneous and least synchronized network, which was also the most stable in terms of population and community fluctuations. In contrast, homogeneous disturbance destabilized the community, enhancing spatial synchronization. Intense disturbances always reduced spatial β diversity, indicating that strong perturbations could destabilize communities via biotic homogenization regardless of their spatial structure. Our findings corroborated theoretical predictions, emphasizing the importance of spatially heterogeneous disturbances in promoting stability by amplifying asynchronous spatial and temporal fluctuations in population and community abundance. In contrast to other networks, synchrony networks are vulnerable to the removal of most peripheral nodes, which are less synchronized, but may contribute more to stability than other nodes by dampening large fluctuations in species abundance. Our findings suggest that climate change and direct anthropogenic disturbance can compromise the stability of ecological communities through combined effects on diversity and synchrony, as well as further affecting ecosystems through habitat loss.
Collapse
Affiliation(s)
- Caterina Mintrone
- Department of Biology, University of Pisa, Pisa, Italy
- CoNISMa, Rome, Italy
| | - Luca Rindi
- Department of Biology, University of Pisa, Pisa, Italy
- CoNISMa, Rome, Italy
| | | |
Collapse
|
46
|
Schloss PD. Rarefaction is currently the best approach to control for uneven sequencing effort in amplicon sequence analyses. mSphere 2024; 9:e0035423. [PMID: 38251877 PMCID: PMC10900887 DOI: 10.1128/msphere.00354-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 12/18/2023] [Indexed: 01/23/2024] Open
Abstract
Considering it is common to find as much as 100-fold variation in the number of 16S rRNA gene sequences across samples in a study, researchers need to control for the effect of uneven sequencing effort. How to do this has become a contentious question. Some have argued that rarefying or rarefaction is "inadmissible" because it omits valid data. A number of alternative approaches have been developed to normalize and rescale the data that purport to be invariant to the number of observations. I generated community distributions based on 12 published data sets where I was able to assess the ability of multiple methods to control for uneven sequencing effort. Rarefaction was the only method that could control for variation in uneven sequencing effort when measuring commonly used alpha and beta diversity metrics. Next, I compared the false detection rate and power to detect true differences between simulated communities with a known effect size using various alpha and beta diversity metrics. Although all methods of controlling for uneven sequencing effort had an acceptable false detection rate when samples were randomly assigned to two treatment groups, rarefaction was consistently able to control for differences in sequencing effort when sequencing depth was confounded with treatment group. Finally, the statistical power to detect differences in alpha and beta diversity metrics was consistently the highest when using rarefaction. These simulations underscore the importance of using rarefaction to normalize the number of sequences across samples in amplicon sequencing analyses. IMPORTANCE Sequencing 16S rRNA gene fragments has become a fundamental tool for understanding the diversity of microbial communities and the factors that affect their diversity. Due to technical challenges, it is common to observe wide variation in the number of sequences that are collected from different samples within the same study. However, the diversity metrics used by microbial ecologists are sensitive to differences in sequencing effort. Therefore, tools are needed to control for the uneven levels of sequencing. This simulation-based analysis shows that despite a longstanding controversy, rarefaction is the most robust approach to control for uneven sequencing effort. The controversy started because of confusion over the definition of rarefaction and violation of assumptions that are made by methods that have been borrowed from other fields. Microbial ecologists should use rarefaction.
Collapse
Affiliation(s)
- Patrick D. Schloss
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, Michigan, USA
| |
Collapse
|
47
|
Dittoe DK, Feye KM, Ovall C, Thompson HA, Ricke SC. Exploiting the microbiota of organic and inorganic acid-treated raw poultry products to improve shelf-life. Front Microbiol 2024; 15:1348159. [PMID: 38476936 PMCID: PMC10927844 DOI: 10.3389/fmicb.2024.1348159] [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: 02/06/2024] [Indexed: 03/14/2024] Open
Abstract
Introduction Targeted amplicon sequencing of the 16S rRNA delineates the complex microbial interactions that occur during food spoilage, providing a tool to intensively screen microbiota response to antimicrobial processing aids and interventions. The current research determines the microbiota and spoilage indicator (total aerobes and lactic acid bacteria; LAB) response to inorganic and organic antimicrobial intervention use on the shelf-life of fresh, never-frozen, skin-on, bone-in chicken wings. Methods Wings (n=200) were sourced from local processor and either not treated (NT) or treated with 15-s dips of tap water (TW), organic (peracetic acid; PAA), inorganic acids (sodium bisulfate; SBS), and their combination (SBS + PAA). Wings were stored (4°C) and rinsed in neutralizing Buffered Peptone Water (BPW) for 1 min on d 0, 7, 14, and 21 post-treatment. Spoilage indicators, aerobic mesophiles and LAB, were quantified from rinsates. Genomic DNA of d 14 and 21 rinsates were extracted, and V4 of 16S rRNA gene was sequenced. Sequences were analyzed using QIIME2.2019.7. APC and LAB counts were reported as Log10 CFU/g of chicken and analyzed in R Studio as a General Linear Model using ANOVA. Pairwise differences were determined using Tukey's HSD (P£0.05). Results Spoilage was indicated for all products by day 21 according to APC counts (>7 Log10 CFU/g); however, wings treated with SBS and SBS + PAA demonstrated a 7-day extended shelf-life compared to those treated with NT, TW, or PAA. The interaction of treatment and time impacted the microbial diversity and composition (p < 0.05), with those treated with SBS having a lower richness and evenness compared to those treated with the controls (NT and TW; p < 0.05, Q < 0.05). On d 14, those treated with SBS and SBS + PAA had lower relative abundance of typical spoilage population while having a greater relative abundance of Bacillus spp. (~70 and 50% of population; ANCOM p < 0.05). By d 21, the Bacillus spp. populations decreased below 10% of the population among those treated with SBS and SBS + PAA. Discussion Therefore, there are differential effects on the microbial community depending on the chemical intervention used with organic and inorganic acids, impacting the microbial ecology differently.
Collapse
Affiliation(s)
- Dana K. Dittoe
- Animal Science, University of Wyoming, Laramie, WY, United States
| | - Kristina M. Feye
- Cell and Molecular Biology Program, University of Arkansas, Fayetteville, AR, United States
| | | | - Hayley A. Thompson
- Center for Food Safety, Department of Food Science, University of Arkansas, Fayetteville, AR, United States
| | - Steven C. Ricke
- Meat Science and Animal Biologics Discovery Program, Animal and Dairy Sciences, University of Wisconsin, Madison, WI, United States
| |
Collapse
|
48
|
Quirino DF, Marcondes MI, de Oliveira KR, Guimarães SEF, da Silva JS, Suen G, Rossi LE, Cunha CS, Mantovani HC, Rotta PP. Comparison of ruminal microbiota, IL-1β gene variation, and tick incidence between Holstein × Gyr and Holstein heifers in grazing system. Front Microbiol 2024; 15:1132151. [PMID: 38468851 PMCID: PMC10925795 DOI: 10.3389/fmicb.2024.1132151] [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: 12/26/2022] [Accepted: 02/13/2024] [Indexed: 03/13/2024] Open
Abstract
Introduction The variation in bacterial communities among breeds has been previously reported and may be one of the reasons why Holstein × Gyr dairy heifers have better development in grazing systems in tropical conditions. This study aimed to explore the ruminal microbiota composition, the IL-1β gene variation, tick incidence, and blood parameters of Holstein × Gyr (½ Holstein × ½ Gyr) and Holstein heifers grazing intensely managed Guinea grass (Panicum maximum Jacq. cv. Mombaça). Methods Sixteen heifers were divided into two groups consisting of 8 Holstein × Gyr and 8 Holstein heifers. The experimental period was comprised of 3 periods of 21 days. Ruminal samples were taken via the stomach tube technique. The sequencing of the V4 hypervariable region of the 16S rRNA gene was performed using the Illumina MiSeq platform. Counting and collection of ticks were conducted each 21 days. Blood and skeletal muscle tissue biopsies were performed at the end of the experiment. Results Firmicutes were the most abundant phyla present in both breed rumen samples and Bacteroidota showed differences in relative abundance between breed groups, with greater values for Holstein heifers (p < 0.05 with FDR correction). The 10 most abundant unique OTUs identified in each breed included several OTUs of the genus Prevotella. Holstein heifers had a greater tick count and weight (9.8 ticks/animal and 1.6 g/animal, respectively) than Holstein × Gyr (2.56 ticks/animal and 0.4 g/animal, respectively). We found nucleotide substitutions in the IL-1β gene that might be related to adaptation and resistance phenotypes to tick infestation in Holstein × Gyr heifers. Blood concentrations of urea, albumin, insulin-like growth factor 1, triiodothyronine, and thyroxine were greater in Holstein × Gyr than in Holstein heifers. Conclusion Adaptations in Holstein × Gyr heifers such as ruminal microbiota, tick resistance, nucleotide substitutions in IL-1β gene, and hormone concentration suggest a better energy metabolism and thermoregulation resulting in better performance in tropical grazing systems.
Collapse
Affiliation(s)
| | | | | | | | | | - Garret Suen
- Department of Bacteriology, University of Wisconsin, Madison, WI, United States
| | - Letícia Elisa Rossi
- Department of Microbiology, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Camila Soares Cunha
- School of Veterinary Medicine and Animal Science, Universidade Federal de Mato Grosso do Sul, Campo Grande, Mato Grosso do Sul, Brazil
| | | | - Polyana Pizzi Rotta
- Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| |
Collapse
|
49
|
Guilherme-Fernandes J, Aires T, Fonseca AJM, Yergaliyev T, Camarinha-Silva A, Lima SAC, Maia MRG, Cabrita ARJ. Squid meal and shrimp hydrolysate as novel protein sources for dog food. Front Vet Sci 2024; 11:1360939. [PMID: 38450029 PMCID: PMC10915000 DOI: 10.3389/fvets.2024.1360939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Accepted: 02/08/2024] [Indexed: 03/08/2024] Open
Abstract
The world's growing pet population is raising sustainability and environmental concerns for the petfood industry. Protein-rich marine by-products might contribute to mitigating negative environmental effects, decreasing waste, and improving economic efficiency. The present study evaluated two marine by-products, squid meal and shrimp hydrolysate, as novel protein sources for dog feeding. Along with the analysis of chemical composition and antioxidant activity, palatability was evaluated by comparing a commercial diet (basal diet) and diets with the inclusion of 150 g kg-1 of squid meal or shrimp hydrolysate using 12 Beagle dogs (2.2 ± 0.03 years). Two in vivo digestibility trials were conducted with six dogs, three experimental periods (10 days each) and three dietary inclusion levels (50, 100 and 150 g kg-1) of squid meal or shrimp hydrolysate in place of the basal diet to evaluate effects of inclusion level on apparent total tract digestibility (ATTD), metabolizable energy content, fecal characteristics, metabolites, and microbiota. Both protein sources presented higher protein and methionine contents than ingredients traditionally used in dog food formulation. Shrimp hydrolysate showed higher antioxidant activity than squid meal. First approach and taste were not affected by the inclusion of protein sources, but animals showed a preference for the basal diet. Effects on nutrient intake reflected the chemical composition of diets, and fecal output and characteristics were not affected by the increasing inclusion levels of both protein sources. The higher ATTD of dry matter, most nutrients and energy of diets with the inclusion of both by-products when compared to the basal diet, suggests their potential to be included in highly digestible diets for dogs. Although not affected by the inclusion level of protein sources, when compared to the basal diet, the inclusion of squid meal decreased butyrate concentration and shrimp hydrolysate increased all volatile fatty acids, except butyrate. Fecal microbiota was not affected by squid meal inclusion, whereas inclusion levels of shrimp hydrolysate significantly affected abundances of Oscillosperaceae (UCG-005), Firmicutes and Lactobacillus. Overall, results suggest that squid meal and shrimp hydrolysate constitute novel and promising protein sources for dog food, but further research is needed to fully evaluate their functional value.
Collapse
Affiliation(s)
- Joana Guilherme-Fernandes
- REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Tiago Aires
- SORGAL, Sociedade de Óleos e Rações S.A., Lugar da Pardala, S. João de Ovar, Portugal
| | - António J. M. Fonseca
- REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Timur Yergaliyev
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Amélia Camarinha-Silva
- HoLMiR – Hohenheim Center for Livestock Microbiome Research, University of Hohenheim, Stuttgart, Germany
- Institute of Animal Science, University of Hohenheim, Stuttgart, Germany
| | - Sofia A. C. Lima
- REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Margarida R. G. Maia
- REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| | - Ana R. J. Cabrita
- REQUIMTE, LAQV, ICBAS, School of Medicine and Biomedical Sciences, University of Porto, Porto, Portugal
| |
Collapse
|
50
|
Tsukimi T, Obana N, Shigemori S, Arakawa K, Miyauchi E, Yang J, Song I, Ashino Y, Wakayama M, Soga T, Tomita M, Ohno H, Mori H, Fukuda S. Genetic mutation in Escherichia coli genome during adaptation to the murine intestine is optimized for the host diet. mSystems 2024; 9:e0112323. [PMID: 38205998 PMCID: PMC10878103 DOI: 10.1128/msystems.01123-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Accepted: 11/15/2023] [Indexed: 01/12/2024] Open
Abstract
Mammalian gut microbes colonize the intestinal tract of their host and adapt to establish a microbial ecosystem. The host diet changes the nutrient profile of the intestine and has a high impact on microbiota composition. Genetic mutations in Escherichia coli, a prevalent species in the human gut, allow for adaptation to the mammalian intestine, as reported in previous studies. However, the extent of colonization fitness in the intestine elevated by genetic mutation and the effects of diet change on these mutations in E. coli are still poorly known. Here, we show that notable mutations in sugar metabolism-related genes (gatC, araC, and malI) were detected in the E. coli K-12 genome just 2 weeks after colonization in the germ-free mouse intestine. In addition to elevated fitness by deletion of gatC, as previously reported, deletion of araC and malI also elevated E. coli fitness in the murine intestine in a host diet-dependent manner. In vitro cultures of medium containing nutrients abundant in the intestine (e.g., galactose, N-acetylglucosamine, and asparagine) also showed increased E. coli fitness after deletion of the genes-of-interest associated with their metabolism. Furthermore, the host diet was found to influence the developmental trajectory of gene mutations in E. coli. Taken together, we suggest that genetic mutations in E. coli are selected in response to the intestinal environment, which facilitates efficient utilization of nutrients abundant in the intestine under laboratory conditions. Our study offers some insight into the possible adaptation mechanisms of gut microbes.IMPORTANCEThe gut microbiota is closely associated with human health and is greatly impacted by the host diet. Bacteria such as Escherichia coli live in the gut all throughout the life of a human host and adapt to the intestinal environment. Adaptive mutations in E. coli are reported to enhance fitness in the mammalian intestine, but to what extent is still poorly known. It is also unknown whether the host diet affects what genes are mutated and to what extent fitness is affected. This study suggests that genetic mutations in the E. coli K-12 strain are selected in response to the intestinal environment and facilitate efficient utilization of abundant nutrients in the germ-free mouse intestine. Our study provides a better understanding of these intestinal adaptation mechanisms of gut microbes.
Collapse
Affiliation(s)
- Tomoya Tsukimi
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Nozomu Obana
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Suguru Shigemori
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Kazuharu Arakawa
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Eiji Miyauchi
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Institute for Molecular and Cellular Regulation, Gunma University, Maebashi, Japan
| | - Jiayue Yang
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Isaiah Song
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Yujin Ashino
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
| | - Masataka Wakayama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
| | - Tomoyoshi Soga
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Faculty of Environment and Information Studies, Keio University, Fujisawa, Japan
| | - Hiroshi Ohno
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Hirotada Mori
- Graduate School of Biological Science, Nara Institute of Science and Technology, Ikoma, Japan
- Institute of Animal Sciences, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Shinji Fukuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
- Systems Biology Program, Graduate School of Media and Governance, Keio University, Fujisawa, Japan
- Transborder Medical Research Center, Institute of Medicine, University of Tsukuba, Tsukuba, Japan
- Gut Environmental Design Group, Kanagawa Institute of Industrial Science and Technology, Kawasaki, Japan
- Laboratory for Regenerative Microbiology, Juntendo University Graduate School of Medicine, Tokyo, Japan
| |
Collapse
|