Article
Microbiology
Kuanguan Huang, Jie Wang, Junhao Huang, Shouke Zhang, Alfried P. Vogler, Quanquan Liu, Yongchun Li, Maowei Yang, You Li, Xuguo Zhou
Summary: In this study, gut microbiota of bamboo-feeding insects were examined to understand their convergent adaptation to extreme diet specialization. Results showed that while both phylogeny and diet can influence the gut microbiome composition, phylogeny primarily drives the convergent adaptation to a highly specialized diet in insects feeding on bamboo.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Medicine, General & Internal
Ramiro Vilchez-Vargas, Jurgita Skieceviciene, Konrad Lehr, Greta Varkalaite, Cosima Thon, Mindaugas Urba, Egidijus Morkunas, Laimutis Kucinskas, Karolina Bauraite, Denny Schanze, Martin Zenker, Peter Malfertheiner, Juozas Kupcinskas, Alexander Link
Summary: This study investigated the gut microbiome composition in twins and found that aging and household sharing were key determinants of microbial similarity and drift.
Article
Biochemistry & Molecular Biology
Oxana M. Drapkina, German A. Ashniev, Olga A. Zlobovskaya, Adel A. Yafarova, Elena Dementeva, Anastasia N. Kaburova, Ivan O. Meshkov, Anna F. Sheptulina, Anton R. Kiselev, Anna Kontsevaya, Linar M. Zhamalov, Sergey N. Koretskiy, Mariya S. Pokrovskaya, Alexandra Akinshina, Anjelica Zagaynova, Mariia Lukashina, Andrey Kirillov, Ivan A. Abramov, Larisa R. Tolkacheva, Irina O. Bikaeva, Evgeniya Glazunova, German A. Shipulin, Maria M. Bobrova, Valentin V. Makarov, Anton A. Keskinov, Vladimir S. Yudin, Sergey M. Yudin
Summary: To further understand the pathogenesis of cardiovascular disease, this study explored the role of gut microbiota in atherosclerotic cardiovascular disease and heart failure, using multiple evaluation methods. The results showed some differences in microbiota composition between different disease groups and the control group, expanding the knowledge on the correlation between gut microbiota and cardiovascular diseases.
Review
Immunology
Boris Vidal-Veuthey, Damariz Gonzalez, Juan P. Cardenas
Summary: This article reviews the literature on the functions of secreted proteins from the gut microbiota and discusses their impact on host physiology and health, as well as how these effects can be utilized for the development of postbiotic products.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Cell Biology
Mariana Delgadinho, Catarina Ginete, Brigida Santos, Joana Mendes, Armandina Miranda, Jocelyne Vasconcelos, Miguel Brito
Summary: Sickle cell disease (SCD) is a common genetic condition worldwide, particularly causing high mortality in children in sub-Saharan Africa. Recent studies have shown that the gut microbiome of SCD patients undergoes changes related to inflammation and vaso-occlusive crises. Differences in the gut microbiome composition were observed between Angolan children with SCD and their healthy siblings, highlighting the importance of further research to improve therapeutic approaches.
JOURNAL OF CELLULAR AND MOLECULAR MEDICINE
(2022)
Article
Environmental Sciences
Beini Deng, Xiaoshang Ru, Ting Wang, Chenxi Zhang, Wanhui Sun, Songchong Lu, Libin Zhang
Summary: This study investigated the changes in gut microbiome composition and metabolites of sea cucumber in different seasons. The results showed significant seasonal variations in gut microbiome of sea cucumber, with higher susceptibility to Vibrio infection in summer and the growth of body wall influenced by stigmasterol and sitosterol.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Microbiology
Jinru Yang, Yuxi Ma, Qiaoyun Tan, Bin Zhou, Dandan Yu, Min Jin, Tao Zhang, Junli Liu, Hongli Liu
Summary: This study found significant differences in gut microbiome composition between pancreatic cancer patients and healthy individuals, and identified Streptococcus as a potential biomarker for early prediction of pancreatic cancer and liver metastasis. This is critical for early diagnosis of diseases.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Ecology
Brian K. Trevelline, Daniel Sprockett, William V. Deluca, Catherine R. Andreadis, Andrew H. Moeller, Christopher M. Tonra
Summary: The gut microbiome of migratory birds undergoes significant changes during migration, with an increase in Proteobacteria and a decrease in microbiome diversity. The microbiome composition becomes more similar among individuals during long-distance migration. Additionally, the gut microbiome of birds preparing for migration is enriched in bacterial pathways involved in vitamin, amino acid, fatty acid biosynthesis, and carbohydrate metabolism.
FUNCTIONAL ECOLOGY
(2023)
Article
Food Science & Technology
Marek Aljewicz, Beata Nalepa, Slawomir Ciesielski
Summary: This study investigated the impact of different β-glucans on the gut microbiome in rats and found that oat β-glucan and curdlan increased the abundance of specific bacterial genera, while a positive correlation was observed between Streptococcus bacteria and the growth rate of rats. Consuming β-glucans at the recommended dose by EFSA did not significantly alter the structure of the gut microbiome in rats.
JOURNAL OF FUNCTIONAL FOODS
(2022)
Article
Plant Sciences
Chakrit Bunyoo, Peerapat Roongsattham, Sirikorn Khumwan, Juthaporn Phonmakham, Passorn Wonnapinij, Arinthip Thamchaipenet
Summary: This study investigated the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions using 16S rRNA amplicon sequencing. The results showed that Proteobacteria was the dominant phylum in duckweed samples. A total of 24 microbial genera were identified as a core microbiome, with consistent proportions across all duckweed subtypes. The diversity of microbial communities decreased after nutrient-deficient stress, but the relative abundance of certain genera significantly increased. Functional prediction of the metagenome data revealed enrichment of essential pathways involved in DAB colonization and biodegradation under stress condition.
Article
Food Science & Technology
Niki Mougiou, Antiopi Tsoureki, Spyros Didos, Ioanna Bouzouka, Sofia Michailidou, Anagnostis Argiriou
Summary: The analysis of table olives microbiome using next-generation sequencing has provided valuable information about the microbial community composition of this popular fermented food. This study used 16S and 18S rRNA sequencing to evaluate the microbial communities of table olives from five Greek popular cultivars, fermented by Greek or Spanish style. The results showed that different curing and fermentation methods had an impact on the microbial composition and biochemical properties of the olives.
Article
Microbiology
Jason A. Rothman, Jenna L. Riis, Katrina R. Hamilton, Clancy Blair, Douglas A. Granger, Katrine L. Whiteson
Summary: Human oral microbial communities have significant implications for oral and systemic health due to their diversity. Understanding the differences between healthy and dysbiotic oral microbiomes is important, especially within and between families. This study investigates the changes in oral microbiome composition within individuals and the impact of factors such as environmental tobacco smoke exposure, metabolic regulation, inflammation, and antioxidant potential. The findings reveal differences in oral microbiomes between children and caregivers, with shared diversity but distinct differences, and highlight the associations between the oral microbiome and various salivary markers.
Article
Microbiology
Gleyciane Machado da Costa, Savio Souza Costa, Rafael Azevedo Barauna, Bruno Pureza Castilho, Izabel Cruz Pinheiro, Artur Silva, Ana Paula Schaan, Andrea Ribeiro-dos-Santos, Diego Assis das Gracas
Summary: The study reveals that human activities, such as the construction of a highway, have impacted the microbial communities in the Amazonian mangroves and resulted in a loss of biodiversity.
Article
Biochemistry & Molecular Biology
Apostolos Galaris, Dionysios Fanidis, Elli-Anna Stylianaki, Vaggelis Harokopos, Alexandra-Styliani Kalantzi, Panagiotis Moulos, Antigone S. Dimas, Pantelis Hatzis, Vassilis Aidinis
Summary: The microbiome is important for tissue homeostasis in health and disease. Dysbiosis of the gut microbiome is related to autoimmune and metabolic diseases, while high-fat diets and obesity affect microbiome diversity and complexity, thus modulating pathophysiology. Obesity increases microbial complexity in the gut, liver, and lung, with the lungs showing the most significant changes in microbial diversity.
Article
Immunology
Xiaolin Liu, Nina van Beek, Aleksa Cepic, Nadia A. Andreani, Cecilia J. Chung, Britt M. Hermes, Kaan Yilmaz, Sandrine Benoit, Kossara Drenovska, Sascha Gerdes, Regine Glaeser, Matthias Goebeler, Claudia Guenther, Anabelle von Georg, Christoph M. Hammers, Maike M. Holtsche, Franziska Huebner, Dimitra Kiritsi, Franziska Schauer, Beke Linnenmann, Laura Huilaja, Kaisa Tasanen-Maatta, Snejina Vassileva, Detlef Zillikens, Christian D. Sadik, Enno Schmidt, Saleh Ibrahim, John F. Baines
Summary: Bullous pemphigoid patients have altered gut microbiota composition and function, with decreased microbial diversity and overall changed microbial community. Disease-associated gut microbial features, including reduced Faecalibacterium prausnitzii and increased pathways related to gamma-aminobutyric acid metabolism, are observed in BP patients. These findings suggest that gut microbiota alterations may play a role in the development of bullous pemphigoid.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Microbiology
Erki Aun, Veljo Kisand, Mailis Laht, Kaidi Telling, Piret Kalmus, Ulo Vali, Age Brauer, Maido Remm, Tanel Tenson
Summary: This study characterized the population structure, drug resistance mechanisms, and virulence genes of Enterococcus isolates in Estonia. The findings revealed closely related strains isolated from different host species, indicating potential interspecies spread of strains and transfer of antibiotic resistance. Genomic context analysis of the resistance genes showed frequent association with plasmids and mobile genetic elements, suggesting the occurrence of transfer events.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Microbiology
Liisi Talas, Normunds Stivrins, Siim Veski, Leho Tedersoo, Veljo Kisand
Summary: The study reveals the diversity and changes in fungal communities in lake sediments throughout the Holocene period. It shows that plankton parasitic fungi became more diverse in the last few millennia, potentially in response to a cooler climate. Major shifts in fungal communities, particularly in plankton parasites and mycorrhizal fungi, occurred during the Late Holocene and Latest Holocene periods, possibly influenced by increased transfer rates of plant material and human impact.
Article
Microbiology
Matthias Hoetzinger, Emelie Nilsson, Rahaf Arabi, Christofer M. G. Osbeck, Benjamin Pontiller, Geoffrey Hutinet, Oliver W. Bayfield, Sachia Traving, Veljo Kisand, Daniel Lundin, Jarone Pinhassi, Mathias Middelboe, Karin Holmfeldt
Summary: This study isolated novel phage genera and species during a Baltic Sea mesocosm experiment, some of which were found to contain gene sets potentially coding for the synthesis of modified nucleotides and glycosylation of bacterial cell surface components. Additionally, phages isolated from a Rheinheimera strain showed high genetic similarity to previously isolated genotypes, pointing to genomic consistency in this population. The investigated phages were mainly detected after a phytoplankton bloom peak in the mesocosm experiment, indicating a potential influence on the succession of heterotrophic bacteria associated with phytoplankton blooms in the Baltic Proper during summer months.
ENVIRONMENTAL MICROBIOLOGY
(2021)
Article
Geography, Physical
Ilmar Tonno, Liisi Talas, Rene Freiberg, Anu Kisand, Simon Belle, Normunds Stivrins, Tiiu Alliksaar, Atko Heinsalu, Siim Veski, Veljo Kisand
Summary: Understanding the long-term dynamics of ecological communities is crucial for explaining present-day biodiversity patterns and predicting future scenarios. Recent studies analyzed changes in a temperate lake ecosystem over the past 14.5 kyr, finding that both climate change and vegetation change impact the dynamics of phototrophs.
QUATERNARY SCIENCE REVIEWS
(2021)
Review
Environmental Sciences
J. Pawlowski, K. Bruce, K. Panksep, F. Aguirre, S. Amalfitano, L. Apotheloz-Perret-Gentil, T. Baussant, A. Bouchez, L. Carugati, K. Cermakova, T. Cordier, C. Corinaldesi, F. O. Costa, R. Danovaro, A. Dell'Anno, S. Duarte, U. Eisendle, B. J. D. Ferrari, F. Frontalini, L. Fruehe, A. Haegerbaeumer, V Kisand, A. Krolicka, A. Lanzen, F. Leese, F. Lejzerowicz, E. Lyautey, I Macek, M. Sagova-Mareckova, J. K. Pearman, X. Pochon, T. Stoeck, R. Vivien, A. Weigand, S. Fazi
Summary: Environmental DNA (eDNA) metabarcoding is transforming aquatic biomonitoring by sequencing DNA/RNA to identify entire communities within a targeted group. Most studies have focused on water eDNA and macroinvertebrate samples, but eDNA metabarcoding has also been applied to soft sediment samples, especially for microbial or meiofaunal communities. Compared to traditional methods, eDNA metabarcoding offers advantages for assessing sediment environmental quality. However, there is a need for standardization to improve robustness and comparability. This review focuses on sampling, preservation, and DNA extraction protocols for sediment eDNA metabarcoding, aiming to identify best practices and promote harmonization for future benthic monitoring.
SCIENCE OF THE TOTAL ENVIRONMENT
(2022)
Article
Agriculture, Dairy & Animal Science
Triin Tedersoo, Mati Roasto, Mihkel Maesaar, Veljo Kisand, Marina Ivanova, Kadrin Meremae
Summary: Since 2005, campylobacteriosis has been the most commonly reported gastrointestinal infection in humans in the European Union. Poultry meat is a major source of both sporadic campylobacter infections and food-borne outbreaks in the EU. Different strains of Campylobacter have been identified, and it is likely that human infections in Estonia are caused by imported fresh broiler chicken meat.
Article
Microbiology
Triin Tedersoo, Mati Roasto, Mihkel Maesaar, Liidia Hakkinen, Veljo Kisand, Marina Ivanova, Marikki Heidi Valli, Kadrin Meremae
Summary: This study investigated the antimicrobial resistance of Campylobacter isolates from fresh broiler chicken meat and human clinical isolates in Estonia. The results showed high antibiotic resistance in Campylobacter spp. from Lithuanian and Latvian-origin broiler chicken meat and Estonian clinical isolates.
Article
Geosciences, Multidisciplinary
Sten Anslan, Wengang Kang, Katharina Dulias, Bernd Wuennemann, Paula Echeverria-Galindo, Nicole Boerner, Anja Schwarz, Yongqin Liu, Keshao Liu, Sven Kuenzel, Veljo Kisand, Patrick Rioual, Ping Peng, Junbo Wang, Liping Zhu, Miguel Vences, Antje Schwalb
Summary: Lake sediments are valuable archives for tracking environmental and biotic changes. This study compared diatom valve records with diatom sedimentary ancient DNA (sedaDNA) metabarcoding data from the same sediment core, revealing similar diatom richness and community patterns. However, mismatches in taxonomic composition existed between the two data sets, likely due to dissolution issues and the lack of reference sequences in public databases. The study also identified significant drivers for diatom richness and community structure, with a strong shift after 1950 CE possibly associated with environmental changes on the Tibetan Plateau.
FRONTIERS IN EARTH SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Carmen Kivistik, Helen Tammert, Veljo Kisand, Kairi Kairo, Daniel P. R. Herlemann
Summary: This study investigates the responses of the gastrointestinal bacterial community in aquatic snails to dietary changes and changes in environmental conditions, and finds that the composition of the bacterial community is affected by salinity and food source. In addition, the presence of antibiotics disrupts the self-regulating mechanism of the host and results in decreased energy reserves.
Article
Fisheries
Alfonso Diaz-Suarez, Kristina Noreikiene, Veljo Kisand, Oksana Burimski, Roland Svirgsden, Mehis Rohtla, Mikhail Ozerov, Riho Gross, Markus Vetemaa, Anti Vasemagi
Summary: The Northern pike population on the Island of Saaremaa, Estonia, shows temporal stability in genetic structure between geographically close locations, with reduced diversity in the north-western populations. There is a clear differentiation between the north-western and Gulf of Riga spawning grounds. These findings suggest that limited dispersal and natal homing behavior in Baltic pike promote the existence of temporally stable genetic divergence at small geographical scales, which is important for local adaptations. Therefore, conservation and management efforts should focus on preserving existing genetic differences and avoiding actions that increase genetic homogenization.
FISHERIES RESEARCH
(2022)
Article
Microbiology
Carmen Kivistik, Kairi Kairo, Helen Tammert, Inna M. Sokolova, Veljo Kisand, Daniel P. R. Herlemann
Summary: Environmental disturbances, such as changes in salinity, have an influence on the bacterial community within the gastrointestinal tract of the Ampullaceana balthica gastropod. A shift to higher salinity levels caused a disruption in energy homeostasis and a change in the gastrointestinal bacterial community composition. This highlights the importance of salinity thresholds, specifically around salinity 3, which may affect the intestinal microbiome of organisms in the face of sea-level rise and salinization of freshwater bodies.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Environmental Sciences
Peeter Laas, Kai Kunnis-Beres, Liisi Talas, Helen Tammert, Ivan Kuprijanov, Daniel P. R. Herlemann, Veljo Kisand
Summary: Ballast water is a major pathway for the introduction of potentially harmful or pathogenic aquatic organisms. Genetic tools can provide accurate and reliable data for monitoring and managing ballast water. Analysis of bacterial communities in ballast water using 16S rRNA gene amplicon sequencing revealed the presence of numerous potentially pathogenic bacterial taxa. UV treatment did not significantly reduce species richness estimates, emphasizing the risk of harmful effects when relying solely on UV treatment for ballast water disinfection.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Microbiology
Owen Higgins, Alexandra Chueiri, Louise O'Connor, Sinead Lahiff, Liam Burke, Dearbhaile Morris, Nicola Maria Pfeifer, Belen Gonzalez Santamarina, Christian Berens, Christian Menge, Manuela Canica, Vera Manageiro, Veljo Kisand, Marwa M. M. Hassan, Brian Gardner, Arnoud H. M. van Vliet, Roberto M. La Ragione, Bruno Gonzalez-Zorn, Terry J. J. Smith
Summary: CTX-M ESBL-producing E. coli is an increasing public health concern, and accurate identification of CTX-M variants is crucial for disease monitoring and treatment. CTX-M-1 and CTX-M-15 are the main ESBL-producing Enterobacteriaceae associated with animal and human infections.
MICROBIOLOGY SPECTRUM
(2023)
Article
Engineering, Environmental
Veljo Kisand, Peeter Laas, Kadi Palmik-Das, Kristel Panksep, Helen Tammert, Leena Albreht, Hille Allemann, Lauri Liepkalns, Katri Vooro, Christian Ritz, Vasili Hauryliuk, Tanel Tenson
Summary: Taking advantage of Estonia's small size and population, a wastewater-based epidemiology approach was used to monitor the spread of SARS-CoV-2, with weekly nation-wide updates released. Results showed that the concentration of the virus in wastewater correlated with the number of COVID-19 infections in the population, and the increase in virus concentration preceded the increase in positive cases by approximately 1.25 weeks (9 days). The surveillance system in Estonia helped inform public health policies and interventions during the COVID-19 pandemic.
Article
Biochemistry & Molecular Biology
Malgorzata Gbylik-Sikorska, Anna Gajda, Monica Felipe-Sotelo, Manuela Canica, Adriana Cabal-Rosel, Tanel Tenson, Marta Korinkova, Kroot Arbo, Veljo Kisand, Gerhard Rab, Martin Brandtner
Summary: The prudent use of veterinary antimicrobial agents in food-producing animals is necessary, but it is crucial to analyze the occurrence of these agents in soil samples to understand their potential impacts on human and animal health and the environment. In this study, a cost-effective and simple analytical method was developed for the determination of twenty-nine antimicrobial compounds from different classes in soil samples.