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      Gut microbiome drives individual memory variation in bumblebees

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          Abstract

          The potential of the gut microbiome as a driver of individual cognitive differences in natural populations of animals remains unexplored. Here, using metagenomic sequencing of individual bumblebee hindguts, we find a positive correlation between the abundance of Lactobacillus Firm-5 cluster and memory retention on a visual discrimination task. Supplementation with the Firm-5 species Lactobacillus apis, but not other non-Firm-5 bacterial species, enhances bees’ memory. Untargeted metabolomics after L. apis supplementation show increased LPA (14:0) glycerophospholipid in the haemolymph. Oral administration of the LPA increases long-term memory significantly. Based on our findings and metagenomic/metabolomic analyses, we propose a molecular pathway for this gut-brain interaction. Our results provide insights into proximate and ultimate causes of cognitive differences in natural bumblebee populations.

          Abstract

          Whether gut microbes drive cognitive differences in natural populations of animals remains unknown. Here, Li et al. demonstrate a causal link between increased symbiotic Lactobacillus Firm-5 species ( L. apis) and improved long-term memory in bumblebees.

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          Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method.

          Kenneth Livak, Thomas D. Schmittgen (2001)
          The two most commonly used methods to analyze data from real-time, quantitative PCR experiments are absolute quantification and relative quantification. Absolute quantification determines the input copy number, usually by relating the PCR signal to a standard curve. Relative quantification relates the PCR signal of the target transcript in a treatment group to that of another sample such as an untreated control. The 2(-Delta Delta C(T)) method is a convenient way to analyze the relative changes in gene expression from real-time quantitative PCR experiments. The purpose of this report is to present the derivation, assumptions, and applications of the 2(-Delta Delta C(T)) method. In addition, we present the derivation and applications of two variations of the 2(-Delta Delta C(T)) method that may be useful in the analysis of real-time, quantitative PCR data. Copyright 2001 Elsevier Science (USA).
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            Fast and sensitive protein alignment using DIAMOND.

            Benjamin Buchfink, Chao Xie, Daniel Huson (2015)
            The alignment of sequencing reads against a protein reference database is a major computational bottleneck in metagenomics and data-intensive evolutionary projects. Although recent tools offer improved performance over the gold standard BLASTX, they exhibit only a modest speedup or low sensitivity. We introduce DIAMOND, an open-source algorithm based on double indexing that is 20,000 times faster than BLASTX on short reads and has a similar degree of sensitivity.
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              CD-HIT: accelerated for clustering the next-generation sequencing data

              Limin Fu, Beifang Niu, Zhengwei Zhu … (2012)
              Summary: CD-HIT is a widely used program for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. In response to the rapid increase in the amount of sequencing data produced by the next-generation sequencing technologies, we have developed a new CD-HIT program accelerated with a novel parallelization strategy and some other techniques to allow efficient clustering of such datasets. Our tests demonstrated very good speedup derived from the parallelization for up to ∼24 cores and a quasi-linear speedup for up to ∼8 cores. The enhanced CD-HIT is capable of handling very large datasets in much shorter time than previous versions. Availability: http://cd-hit.org. Contact: liwz@sdsc.edu Supplementary information: Supplementary data are available at Bioinformatics online.
              Article 0 comments Cited 2529 times – based on 0 reviews     Review now
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                Author and article information

                Contributors
                Wei Zhao:
                ORCID: http://orcid.org/0000-0001-9495-8508
                zhaow@jiangnan.edu.cn
                Journal
                Journal ID (nlm-ta): Nat Commun
                Journal ID (iso-abbrev): Nat Commun
                Title: Nature Communications
                Publisher: Nature Publishing Group UK (London )
                ISSN (Electronic): 2041-1723
                Publication date (Electronic): 25 November 2021
                Publication date PMC-release: 25 November 2021
                Publication date Collection: 2021
                Volume: 12
                Electronic Location Identifier: 6588
                Affiliations
                [1 ]GRID grid.258151.a, ISNI 0000 0001 0708 1323, State Key Laboratory of Food Science and Technology, School of Food Science and Technology, , Jiangnan University, ; Wuxi, Jiangsu 214122 China
                [2 ]GRID grid.10858.34, ISNI 0000 0001 0941 4873, Ecology and Genetics Research Unit, , University of Oulu, ; Oulu, Finland
                [3 ]GRID grid.4868.2, ISNI 0000 0001 2171 1133, School of Biological and Behavioural Sciences, , Queen Mary University of London, ; London, E1 4NS UK
                [4 ]GRID grid.459328.1, ISNI 0000 0004 1758 9149, Affiliated Hospital of Jiangnan University, ; Wuxi, Jiangsu 214122 China
                Author information
                http://orcid.org/0000-0003-1214-1137
                http://orcid.org/0000-0003-2517-6179
                http://orcid.org/0000-0002-1401-9728
                http://orcid.org/0000-0001-8153-1732
                http://orcid.org/0000-0001-9495-8508
                Article
                Publisher ID: 26833
                DOI: 10.1038/s41467-021-26833-4
                PMC ID: 8616916
                PubMed ID: 34824201
                SO-VID: c282a77e-250a-4abf-8fde-ac86bde5a7cb
                Copyright © © The Author(s) 2021
                License:

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                Date received : 26 May 2021
                Date accepted : 25 October 2021
                Funding
                Funded by: National Key Research and Development Program of China (No. 2017YFC1601704); National Natural Science Foundation of China (No. 1522044, 31671909 and 31772034); Program of the Jiangsu Key Laboratory of Advanced Food Manufacturing Equipment & Technology (No. FMZ201904); National First-Class Discipline Program of Food Science and Technology (No. JUFSTR20180205); China Postdoctoral Science Foundation (No. 2019M651709); Natural Science Foundation for Youths of Jiangsu Province, China (No. BK20190598).
                Categories
                Subject: Article
                Custom metadata
                issue-copyright-statement © The Author(s) 2021

                ScienceOpen disciplines: Uncategorized
                Keywords: long-term memory,metagenomics,microbiome
                Data availability:
                ScienceOpen disciplines: Uncategorized
                Keywords: long-term memory, metagenomics, microbiome

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