Article
Microbiology
Anand B. Karki, Bhuwan Khatri, Mohamed K. Fakhr
Summary: RNA-seq was used to analyze the differentially expressed genes (DEGs) in C. coli HC2-48 and C. jejuni OD2-67 transcriptomes under different temperature conditions. In C. coli HC2-48, genes involved in flagellar assembly were significantly impacted by low temperatures (4°C), while genes related to the ribosome and ribonucleoprotein complex were modulated in C. jejuni OD2-67 at 4°C. Although more DEGs were observed in the chicken juice medium compared to Mueller-Hinton broth, there were no common genes expressed at all incubation times, indicating that the food matrix environment is not the sole determinant of differential expression in Campylobacter spp. at low temperatures.
Article
Biotechnology & Applied Microbiology
Deirdre M. Prendergast, Helen Lynch, Paul Whyte, Olwen Golden, Declan Murphy, Montserrat Gutierrez, Juliana Cummins, Dayle Johnston, Declan Bolton, Aidan Coffey, Brigid Lucey, Lisa O'Connor, William Byrne
Summary: This study used whole genome sequencing to analyze the genomic diversity of Campylobacter jejuni and identified virulence genes. The results suggest that caecal colonization is the main source of C. jejuni contamination in broiler carcasses, rather than cross-contamination from other batches or the environment.
JOURNAL OF APPLIED MICROBIOLOGY
(2022)
Review
Immunology
Se-Hun Kim, Ramachandran Chelliah, Sudha Rani Ramakrishnan, Ayyappasamy Sudalaiyadum Perumal, Woo-Suk Bang, Momna Rubab, Eric Banan-Mwine Daliri, Kaliyan Barathikannan, Fazle Elahi, Eunji Park, Hyeon Yeong Jo, Su-Bin Hwang, Deog Hwan Oh
Summary: Campylobacter spp. are the leading cause of bacterial colon infections in humans globally, and their stress-adaptation mechanisms differ from other enteropathogenic bacteria, allowing them to survive in diverse environments and enhance their resistance mechanisms.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2021)
Review
Microbiology
Pongthorn Pumtang-on, Timothy J. Mahony, Rodney A. Hill, Thiru Vanniasinkam
Summary: Campylobacter jejuni infection linked to contaminated poultry products is a leading cause of human enteric illness worldwide. Vaccination of chickens is a potential strategy to control C. jejuni colonization, but identifying the most effective formulation remains a challenge due to variability in reported vaccine efficacies. A systematic review comparing C. jejuni vaccine studies found total outer membrane proteins and cysteine ABC transporter substrate-binding protein to be among the most efficacious vaccine antigen candidates, highlighting the need for increased consistency in study design and reporting in poultry to enable robust comparisons of vaccine candidates.
Review
Chemistry, Applied
Murat Gurbuz, Burcu Irem Omurtag Korkmaz
Summary: Poultry is a rapidly growing industry, but concerns about food safety and the presence of bacteria like Campylobacter in poultry remain. The discovery of new antimicrobials, such as eugenol, is important for ensuring the safety of poultry meat. However, further research is needed to determine the specific applications and effectiveness of eugenol as a food preservative in poultry meat safety.
Article
Microbiology
Silvija Soprek, Josip Ujevic, Gordan Kompes, Luka Jurinovic, Arjana Tambic Andrasevic
Summary: In the era of growing antimicrobial resistance, a new perspective using a One Health approach was taken to explore possible explanations for the continuous spread of AMR. C. jejuni ST-21CC was chosen as the pathogen due to its natural transformability, high incidence of infections, and emerging resistance worldwide. Analysis of genomic and phenotypic data revealed high fluoroquinolone resistance in ST-21CC strains, with more diverse genetic backgrounds observed in wild birds.
Article
Microbiology
Hiroshi Asakura, Shiori Yamamoto, Kazuhiro Yamada, Jun Kawase, Hiromi Nakamura, Kou-ichiro Abe, Yoshimasa Sasaki, Tetsuya Ikeda, Ryohei Nomoto
Summary: Campylobacter jejuni and C. coli are major causes of gastrointestinal illnesses transmitted to humans mainly through chicken meats. This study examined the levels of bacterial contamination in retail chicken meats in Japan and found that 45.7% of the samples were positive, with 8.4% exceeding the safe limit. Bacterial counts were higher in fall compared to spring and summer, and younger slaughtered chickens were more contaminated. The study also identified antimicrobial resistance genes and clonal complexes of C. jejuni isolates.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Microbiology
Silvija Soprek, Sanja Duvnjak, Gordan Kompes, Luka Jurinovic, Arjana Tambic Andrasevic
Summary: Campylobacteriosis is a global health challenge due to increasing antimicrobial resistance in Campylobacter jejuni. A study compared the antimicrobial resistance and genotype distribution between strains isolated from stool and primary sterile sites. The study found a high rate of fluoroquinolone resistance in C. jejuni, with a lower resistance rate in invasive isolates. The isolates found in primary sterile samples had lower resistance rates and showed more genetic uniformity.
Article
Microbiology
Sophie Chagneau, Marie-Lou Gaucher, William P. Theriault, Philippe Fravalo, Alexandre Thibodeau
Summary: This study investigates the relationship between two different C. jejuni strains in poultry and their impact on gut colonization and liver spread. The findings suggest that there is both commensalism and competition between the strains, and the mode of colonization and spread differs depending on the strain. Further research is needed to elucidate the mechanisms of commensalism and competition between strains in order to develop appropriate control strategies for farms.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Food Science & Technology
Shanwei Tong, Luyao Ma, Jennifer Ronholm, William Hsiao, Xiaonan Lu
Summary: Campylobacter is a leading cause of bacterial gastroenteritis worldwide, and whole genome sequencing has been proven to be a robust and efficient tool for monitoring this microbe in food chain surveillance.
CURRENT OPINION IN FOOD SCIENCE
(2021)
Article
Microbiology
Andrea Laconi, Roberta Tolosi, Ilenia Drigo, Luca Bano, Alessandra Piccirillo
Summary: This study assessed the ability of C. jejuni and C. coli strains isolated from diseased poultry to form biofilm. The results showed that C. jejuni strains were classified as no, weak, and moderate biofilm producers, while all C. coli strains were weak producers. Genes involved in chemotaxis, adhesion, and invasion were present in all C. jejuni strains. Further investigations are needed to better understand the genetic determinants involved in extra-intestinal Campylobacter biofilm formation.
VETERINARY MICROBIOLOGY
(2023)
Article
Microbiology
Carla Susana Rodrigues, Paulo Marcel Armendaris, Claudia Valeria Goncalves Cordeiro de Sa, Joao Paulo Amaral Haddad, Cristiano Barros de Melo
Summary: This study aimed to estimate the prevalence of Campylobacter in chicken carcasses from slaughterhouses in three states in southern Brazil, revealing a prevalence of 35.84% with C. jejuni being the main species. While the size of slaughterhouses did not affect the prevalence, significant differences were observed among the three states, with Parana having the lowest prevalence. The results highlight the need for strategies to control this pathogen in Brazil to protect consumer health and maintain the country's position in the international poultry meat market.
CURRENT MICROBIOLOGY
(2021)
Article
Microbiology
Andrea Laconi, Ilenia Drigo, Nicola Palmieri, Lisa Carraro, Elena Tonon, Raffaela Franch, Luca Bano, Alessandra Piccirillo
Summary: The study revealed that Campylobacter isolates from chicken livers possessed a higher number of virulence-associated genes, which might contribute to the development of pathological lesions in these isolates within the host.
VETERINARY MICROBIOLOGY
(2021)
Article
Microbiology
Nagham Anis, Laetitia Bonifait, Segolene Quesne, Louise Bauge, Wissam Yassine, Muriel Guyard-Nicodeme, Marianne Chemaly
Summary: Campylobacter and Salmonella are the two major foodborne zoonotic diseases in Europe, with poultry as the main source of infection. In this study, it was found that the survival of C. jejuni, a type of Campylobacter, was significantly higher when co-cultured with Salmonella. The presence of Salmonella positively affected the survival of C. jejuni, but the extent of the effect depended on the Salmonella serotype, C. jejuni strain, and initial concentration. These findings suggest potential interactions between Salmonella and C. jejuni that need further investigation for a better understanding of their behavior in natural habitats.
Article
Microbiology
Satu Olkkola, Mirko Rossi, Anniina Jaakkonen, Maria Simola, Jouni Tikkanen, Marjaana Hakkinen, Pirkko Tuominen, Otso Huitu, Jukka Niemimaa, Heikki Henttonen, Rauni Kivisto
Summary: The study found that C. jejuni was the only Campylobacter species identified in small wild mammals in Finland and in samples collected near 40 farms, with the highest prevalence in yellow-necked mice and bank voles. Through whole-genome sequencing analysis, it was suggested that C. jejuni strains from voles may represent a new previously undescribed species. The research also showed that the phylogeny of the isolates followed host species-association, rather than origin from either farm or wild captured environments.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Charles Christian Riis Hansen, Aki Jarl Laruson, Jacob Agerbo Rasmussen, Jesus Adrian Chimal Ballesteros, Mikkel-Holger S. Sinding, Gunnar T. T. Hallgrimsson, Menja von Schmalensee, Robert A. A. Stefansson, Kristinn Haukur Skarphedinsson, Aili Lage Labansen, Madis Leivits, Christian Sonne, Rune Dietz, Kim Skelmose, David Boertmann, Igor Eulaers, Michael D. D. Martin, Agnar S. S. Helgason, M. Thomas P. Gilbert, Snaebjorn Palsson
Summary: Divergence in white-tailed eagle populations across Europe and the North-East Atlantic is observed, with the greatest differentiation between island and mainland populations. The island populations have a common ancestry from a mainland population and show signs of inbreeding and little genetic variation. Temporal differences also indicate persistent regional populations despite potential admixture. These patterns may have been shaped by historical events such as glaciation, colonization, human expansion, and persecution.
Article
Multidisciplinary Sciences
Ryan R. Germain, Shaohong Feng, Lucas Buffan, Carlos P. Carmona, Guangii Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: By combining morphological, ecological, and life-history trait data with genomic-based estimates of changing effective population size, this study explores the demographic-based shifts in avian functional diversity over the past million years and under pre-anthropogenic climate warming. The results show that functional diversity remained relatively stable over this period, but significant changes occurred in some key areas of trait space due to changing species abundances. Furthermore, the study identifies the vulnerability of different regions of functional space among taxa, enhancing our understanding of losses of biosphere integrity before human disturbances and contemporary biodiversity loss.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Amanda Bolt Botnen, Mads Bjorn Bjornsen, Antton Alberdi, M. Thomas P. Gilbert, Ostaizka Aizpurua
Summary: As metagenomic studies expand, the challenge of incorporating data from isolated locations or longitudinal time samples arises. This study introduces a simplified method of DNA extraction from faecal material stored on FTA cards and compares it to the traditional freeze-based storage method. The results demonstrate that the simplified extraction method yields higher diversity and an expanded core microbiome, suggesting its viability as an alternative when freeze-based methods are not feasible.
Article
Biochemistry & Molecular Biology
David Diez-del-Molino, Marianne Dehasque, J. Camilo Chacon-Duque, Patricia Pecnerova, Alexei Tikhonov, Albert Protopopov, Valeri Plotnikov, Foteini Kanellidou, Pavel Nikolskiy, Peter Mortensen, Gleb K. Danilov, Sergey Vartanyan, M. Thomas P. Gilbert, Adrian M. Lister, Peter D. Heintzman, Tom van der Valk, Love Dalen
Summary: By analyzing 23 woolly mammoth genomes, researchers have identified genes associated with fixed derived non-synonymous mutations unique to the species and estimated the time of evolution for these mutations. The study found that the woolly mammoth had acquired a broad spectrum of positively selected genes at the time of its origin, including those related to hair and skin development, fat storage and metabolism, and immune system function. The research also revealed ongoing evolution of these phenotypes through positive selection on different sets of genes over the past 700,000 years, as well as relatively recent positive selection on genes related to skeletal morphology, body size, and small ear size.
Article
Biotechnology & Applied Microbiology
Soren B. Hansen, Davide Bozzi, Sarah S. T. Mak, Cecilie G. Clausen, Tue K. Nielsen, Miyako Kodama, Lars H. Hansen, M. Thomas P. Gilbert, Morten T. Limborg
Summary: Obtaining desired phenotypic traits in aquacultural production of Atlantic salmon is still a challenge, and the presence of host-associated microorganisms might contribute to this challenge. Understanding the factors that shape the microbiota is crucial for manipulating it towards desired host traits. In this study, DNA methylation differences associated with a tenacibaculosis outbreak and microbiota displacement in Atlantic salmon were investigated, revealing potential genes involved in host-microbiota interactions and the importance of considering epigenetic factors in manipulating farmed fish microbiota.
Article
Ecology
Jacob A. Rasmussen, Pia Kiilerich, Abdullah S. Madhun, Rune Waagbo, Erik-Jan R. Lock, Lise Madsen, M. Thomas P. Gilbert, Karsten Kristiansen, Morten T. Limborg
Summary: Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform our understanding of adaptive phenotypic traits. This study reveals a strong co-evolution between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations, indicating an interplay between the host and its resident bacteria.
Article
Ecology
Ryan R. Germain, Shaohong Feng, Guangji Chen, Gary R. Graves, Joseph A. Tobias, Carsten Rahbek, Fumin Lei, Jon Fjeldsa, Peter A. Hosner, M. Thomas P. Gilbert, Guojie Zhang, David Nogues-Bravo
Summary: Using whole-genome sequence data, this study reconstructs the demographic histories of 263 bird species over the past million years and identifies networks of interacting morphological and life history traits associated with changes in effective population size (Ne) in response to climate warming and cooling. The results highlight the direct and indirect effects of key traits representing dispersal, reproduction, and survival on long-term demographic responses to climate change, thus identifying the traits most likely to influence population responses to ongoing climate warming.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Genetics & Heredity
Marcela Sandoval-Velasco, Anuradha Jagadeesan, Jazmin Ramos-Madrigal, Maria C. Avila-Arcos, Cesar A. Fortes-Lima, Judy Watson, Erna Johannesdottir, Diana I. Cruz-Davalos, Shyam Gopalakrishnan, J. Victor Moreno-Mayar, Jonas Niemann, Gabriel Renaud, Katharine A. Robson Brown, Helena Bennett, Andrew Pearson, Agnar Helgason, M. Thomas P. Gilbert, Hannes Schroeder
Summary: This article highlights the crucial role of St Helena in suppressing the transatlantic slave trade. The study conducted ancient DNA analyses on 20 individuals whose remains were recovered on the island, revealing that they most likely originated from different source populations between northern Angola and Gabon. The majority of the individuals were male, supporting documented gender bias in the latter phase of the transatlantic slave trade.
AMERICAN JOURNAL OF HUMAN GENETICS
(2023)
Article
Biology
Catia Lucio Pereira, Zeynep Ersoy, M. Thomas P. Gilbert, Dominique Gravel, Miguel B. Araujo, Miguel G. Matias
Summary: Food webs represent interactions between organisms in ecosystems. Matching traits of consumers and resources can help understand these interactions better. However, using environmental DNA (eDNA) for trait matching studies is challenging due to the lack of abundance estimates and trait descriptions. This paper synthesizes recent literature on using eDNA and trait matching to infer trophic interactions, identifying challenges and opportunities for coupled eDNA-trait recording schemes. The case study presented demonstrates that combining eDNA and trait data collection improves the characterization of food webs on various scales. To future-proof eDNA data, it is important to collect new traits or compile existing trait data at relevant spatiotemporal scales.
Article
Multidisciplinary Sciences
Marta Maria Ciucani, Jazmin Ramos-Madrigal, German Hernandez-Alonso, Alberto Carmagnini, Sabhrina Gita Aninta, Xin Sun, Camilla Hjorth Scharff-Olsen, Liam Thomas Lanigan, Ilaria Fracasso, Cecilie G. Clausen, Jouni Aspi, Ilpo Kojola, Laima Baltrunaite, Linas Balciauskas, Jane Moore, Mikael Akesson, Urmas Saarma, Maris Hindrikson, Pavel Hulva, Barbora Cerna Bolfikova, Carsten Nowak, Raquel Godinho, Steve Smith, Ladislav Paule, Sabina Nowak, Robert W. Myslajek, Sabrina Lo Brutto, Paolo Ciucci, Luigi Boitani, Cristiano Vernesi, Hans K. Stenoien, Oliver Smith, Laurent Frantz, Lorenzo Rossi, Francesco Maria Angelici, Elisabetta Cilli, Mikkel-Holger S. Sinding, M. Thomas P. Gilbert, Shyam Gopalakrishnan
Summary: The Sicilian wolf, which lived in isolation on the Sicily island, became extinct in the 1930s-1960s. Genomic analysis of museum specimens revealed that the Sicilian wolf is closely related to the Italian wolf but also carries genetic ancestry from a lineage of Eneolithic and Bronze Age dogs. The Sicilian wolf had lower nucleotide diversity and higher inbreeding compared to the Italian wolf, indicating the effects of a population in a confined island environment.
Article
Microbiology
Yulan Su, Thomas Alter, Greta Goelz
Summary: The aim of this study was to investigate the impact of surrounding viscosity on the expression of motility related genes in Campylobacter jejuni. RNA was extracted from liquid cultures and bacterial cells recovered from the edge and center of a swarming halo. The study found different gene expression patterns and higher energy demand in high viscous media compared to liquid culture, indicating the importance of considering viscosity in motility related studies.
EUROPEAN JOURNAL OF MICROBIOLOGY AND IMMUNOLOGY
(2023)
Review
Biotechnology & Applied Microbiology
Trudy M. Wassenaar, David W. Ussery, Adriana Cabal Rosel
Summary: Omics research involves the collection and analysis of big data, which requires automated approaches. In the field of genomics, specialized software, quality control of input data, and simplification for visualization of results are necessary. Clear communication of big data analyses can be enhanced by novel visualization strategies. The interpretation of findings may be hindered by lack of understanding of analytical tools by microbiologists and limited knowledge of the biology of the microbes under study by researchers.
JOURNAL OF APPLIED MICROBIOLOGY
(2023)
Article
Biology
Edward Rice, Antton Alberdi, James Alfieri, Giridhar Athrey, Jennifer Balacco, Philippe Bardou, Heath Blackmon, Mathieu Charles, Hans Cheng, Olivier Fedrigo, Steven Fiddaman, Giulio Formenti, Laurent Frantz, M. Thomas Gilbert, Cari Hearn, Erich Jarvis, Christophe Klopp, Sofia Marcos, Andrew Mason, Deborah Velez-Irizarry, Luohao Xu, Wesley Warren
Summary: This research presents a pangenome model for domestic chickens consisting of thirty assemblies from different breeds and research lines. It demonstrates how this model can be used to catalogue structural variants in modern breeds and unravel complex nested variations. The study shows that aligning short reads from diverse wild and domestic chickens to this pangenome reduces reference bias and allows for accurate genotyping of complex structural variants.
Article
Biochemistry & Molecular Biology
German Hernandez-Alonso, Jazmin Ramos-Madrigal, Hein van Grouw, Marta Maria Ciucani, Emily Louisa Cavill, Mikkel-Holger S. Sinding, Shyam Gopalakrishnan, George Pacheco, M. Thomas P. Gilbert
Summary: This study used whole-genome sequencing data to investigate the population structure, domestication history, and taxonomy of the rock dove Columba livia. The results revealed the basal position of the West African subspecies, gene-flow between the rock dove's sister species, and proposed a model for the rock dove's evolution based on the refugia theory. Additionally, the study identified at least one domestication event in the Levant that gave rise to all analyzed domestic breeds.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Fisheries
Mikkel Skovrind, George Pacheco, Emil Aputsiaq Flindt Christensen, Shyam Gopalakrishnan, Katharina Fietz, Tore Hejl Holm-Hansen, Filipe Garrett Vieira, Marcus Anders Krag, Henrik Carl, M. Thomas P. Gilbert, Morten Tange Olsen, Peter Rask Moller
Summary: Environmental variation can lead to local adaptations in wild species. In the case of European perch, a specialised brackish water variant has developed in the Baltic Sea region. However, little is known about the mechanisms underlying the perch’s adaptation to the Baltic Sea. Through genetic analysis, it was found that brackish water perch show distinct genetic differences compared to freshwater perch, with higher levels of gene flow. Selection analysis suggests that genomic adaptation played a role in the perch’s colonization of the Baltic Sea.
FISHERIES RESEARCH
(2023)
