Article
Microbiology
Clio Der Sarkissian, Irina M. Velsko, Anna K. Fotakis, Ashild J. Vagene, Alexander Huebner, James A. Fellows Yates
Summary: Ancient metagenomics, like modern metagenomics, deals with degraded DNA in low abundance, requiring specialized measures. Researchers often face challenges with finite sample sizes, experimental design limitations, and ethical considerations.
Article
Microbiology
Nicholas S. Rhoades, Isaac R. Cinco, Sara M. Hendrickson, Mark K. Slifka, Ilhem Messaoudi
Summary: Pregnancy and the postpartum period result in significant changes in the maternal gut microbiome, even in the absence of dietary changes. These changes play an important role in the physiological adaptations required to support fetal growth and maternal health. Understanding the dynamics of the gut microbiome during this period can provide valuable insights into the relationship between microbiome changes and other physiological changes in pregnancy.
MICROBIOLOGY SPECTRUM
(2022)
Article
Environmental Sciences
Xinghua Ding, Wensheng Lan, Aixin Yan, Yiliang Li, Yoko Katayama, Ji-Dong Gu
Summary: The study conducted a metadata analysis on the microbial sequencing data available from NCBI database to determine the diversity, biodeterioration potential, and functionality of stone microbiomes on world cultural heritage sites under different climatic conditions. The microbial communities on stone monuments were found to be associated with climate types, with stone monuments in dry climates showing higher diversity. Functions related to photosynthesis and UV resistance were identified in different climate types. The research highlighted the diverse and self-sustaining nature of these stone-dwelling microbiomes, driven by energy metabolism and biomass accumulation, with biochemical reactions of nitrogen and sulfur cycles being predominant.
JOURNAL OF ENVIRONMENTAL MANAGEMENT
(2022)
Article
Microbiology
M. H. Y. Leung, X. Tong, K. O. Boifot, D. Bezdan, D. J. Butler, D. C. Danko, J. Gohli, D. C. Green, M. T. Hernandez, F. J. Kelly, S. Levy, G. Mason-Buck, M. Nieto-Caballero, D. Syndercombe-Court, K. Udekwu, B. G. Young, C. E. Mason, M. Dybwad, P. K. H. Lee
Summary: The study found that city was the main factor influencing differences in the public transit air microbiome, with diverse taxa driving geography-specific functional potentials. Bacterial strains in different cities showed variations in genes related to resistance and other functions. Human skin, soil, and wastewater were identified as major presumptive sources of resistome in the public transit air, with a significant presence of resistance genes co-located with mobile genetic elements like plasmids. Geographical specificity played a key role in shaping the public transit air microbiome, highlighting the need for global efforts to better understand this built environment.
Article
Microbiology
Hao Fu, Maozhang He, Jinyuan Wu, Yunyan Zhou, Shanlin Ke, Zhe Chen, Qin Liu, Min Liu, Hui Jiang, Lusheng Huang, Congying Chen
Summary: Parturition is a crucial event in the sow reproduction cycle, and studies have shown significant changes in gut microbiota and serum metabolite features from late pregnancy to postpartum. The specific bacterial species, functional capacities, and metabolite features related to lipid, amino acids, and vitamins were found to differ between late pregnancy and postpartum stages in sows.
FRONTIERS IN MICROBIOLOGY
(2021)
Article
Computer Science, Software Engineering
Ivan Sipiran, Patrick Lazo, Cristian Lopez, Milagritos Jimenez, Nihar Bagewadi, Benjamin Bustos, Hieu Dao, Shankar Gangisetty, Martin Hanik, Ngoc-Phuong Ho-Thi, Mike Holenderski, Dmitri Jarnikov, Arniel Labrada, Stefan Lengauer, Roxane Licandro, Dinh-Huan Nguyen, Thang-Long Nguyen-Ho, Luis A. Perez Rey, Bang-Dang Pham, Minh-Khoi Pham, Reinhold Preiner, Tobias Schreck, Quoc-Huy Trinh, Loek Tonnaer, Christoph von Tycowicz, The-Anh Vu-Le
Summary: This paper presents the methods and results of the SHREC'21 track on a dataset of cultural heritage objects, introducing challenges in shape retrieval and cultural retrieval. Ten groups participated with results showing the dominance of learning methods in characterizing 3D objects, but the challenges remain unsolved.
COMPUTERS & GRAPHICS-UK
(2021)
Article
Microbiology
Ellen E. Higginson, M. Abu Sayeed, Joana Pereira Dias, Vignesh Shetty, Mamatha Ballal, Sunil Kumar Srivastava, Ian Willis, Firdausi Qadri, Gordon Dougan, Ankur Mutreja
Summary: Enterotoxigenic Escherichia coli (ETEC) is a significant cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. The gut microbiome may play a role in the resistance or progression to ETEC infection. In this study, the researchers analyzed the gut microbiomes of individuals in Bangladesh infected with ETEC, both symptomatically and asymptomatically. Symptomatic patients had higher bacterial burden, were more likely to be coinfected with other pathogenic bacteria, and had a higher prevalence of antimicrobial resistance genes. The composition of the gut microbiome was different between symptomatic and asymptomatic individuals, providing insight into the impact of the gut microbiome in intestinal infections.
Article
Microbiology
Cecilia G. Flocco, Anika Methner, Franziska Burkart, Alicia Geppert, Joerg Overmann
Summary: Microbiological and biomolecular approaches to cultural heritage research have expanded the scope of research to include provenance inquiry and assessment of environmental impacts in a global context. Tailored methodologies are required due to the unique characteristics and limited access of cultural heritage objects. This review proposes a standardized workflow for studying the microbiome of cultural heritage objects, focusing on bacterial taxa. The aim is to facilitate interdisciplinary inquiry and interactions among the cultural heritage research community.
FRONTIERS IN MICROBIOLOGY
(2023)
Article
Microbiology
Florencia Velez-Cortes, Harris Wang
Summary: Bacterially secreted proteins are crucial for the functioning of bacterial cells and communities. In this study, a computational pipeline was used to predict and analyze the bacterial metasecretome of the human gut, revealing the presence of diverse families of secreted carbohydrate-active enzymes and their distribution across taxonomic groups. By mapping secreted proteins to metagenomic data from endoscopic sampling of the human gastrointestinal tract, specific regions were identified where resident microbes secrete glycosidases. The comprehensive analysis of the metasecretome provides valuable insights for microbiome research and understanding the impact of gut bacteria on human health.
Article
Microbiology
Sarika Jaiswal, Bharti Aneja, Jaisri Jagannadham, Bharati Pandey, Rajender Singh Chhokar, Subhash Chander Gill, Om Parkash Ahlawat, Anuj Kumar, U. B. Angadi, Anil Rai, Ratan Tiwari, Mir Asif Iquebal, Dinesh Kumar
Summary: This study investigates the impact of different cropping patterns on the soil microbial diversity of wheat microbiome. The findings highlight the significant influence of crop rotation on soil microbial diversity and community composition, showcasing the economic and environmental importance of sustainable agricultural practices for food security and ecosystem health.
MICROBIOLOGY SPECTRUM
(2022)
Article
Microbiology
Lingdi Zhang, Jahan Rahman, Matthew Chung, Lauren Lashua, Aubree Gordon, Angel Balmaseda, Guillermina Kuan, Richard Bonneau, Elodie Ghedin
Summary: Based on the analysis of household samples, we found that metagenomic-type analyses of the microbiome can track the transmission of airway bacteria. Microbial communities were more similar between individuals who cohabit in the same household than between individuals from different households. Sharing of bacteria from the airways increased in households with influenza infections compared to control households. However, due to the limited number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.
Article
Microbiology
Erica M. Lopes, Maicon R. Z. Passini, Luciano T. Kishi, Tsute Chen, Bruce J. Paster, Brenda P. F. A. Gomes
Summary: Periodontal and Endodontic diseases are biofilm-related diseases with distinct microbial compositions, indicating potential interactions and communication between the microbiomes of the two sites. The microbial diversity and antibiotic resistance markers differ between infected root canals and periodontal pockets, with the latter showing a higher abundance of species and broader spectrum resistance. The study also identified markers related to systemic diseases in the microbial communities, highlighting the need for further research on the potential implications of cross-infection between endodontic and periodontal diseases.
Review
Microbiology
Laura K. Inglis, Robert A. Edwards
Summary: The microbiome plays a crucial role in ecosystems, and the emergence of metagenomic sequencing techniques has allowed for a more comprehensive study of microbiomes. However, the use of open-access metagenomic data can be challenging due to the lack of metadata, which can be addressed by using algorithms for automatic sorting.
Article
Computer Science, Information Systems
Cristina Portales, Pablo Casanova-Salas, Javier Sevilla, Jorge Sebastian, Arabella Leon, Jose Javier Samper
Summary: Geographical information is becoming a powerful tool for analyzing and visualizing cultural object collections. It allows users to contextualize and understand these objects in ways that resemble our everyday spatial experience, surpassing traditional textual narratives. The SeMap project has created an online resource showcasing over 200,000 cultural objects through spatiotemporal maps, enabling new experiences and perspectives around these objects.
ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION
(2022)
Article
Environmental Sciences
Hannah E. Laue, Yuka Moroishi, Thomas J. Palys, Brian P. Jackson, Juliette C. Madan, Margaret R. Karagas
Summary: Gut bacteria are associated with the impact of environmental exposures on human systems. The study found a correlation between arsenic-metabolizing bacteria in the infant gut microbiome and urinary arsenic excretion. Some arsenic-related gene pathways were associated with arsenic exposure and speciation, with stronger associations observed in infants delivered by caesarean section.
ENVIRONMENTAL RESEARCH
(2022)
Article
Archaeology
E. Boccalon, M. Nocchetti, M. Pica, A. Romani, K. Sterflinger
Summary: In this study, a novel PVA-borax hydrogel containing antimicrobial active ingredients was designed and tested on biodeteriorated stones. The hydrogels with silver nanoparticles and thyme essential oil were found to be the most efficient cleaning systems, opening up new possibilities for bioremediation. The effects of the treatments were assessed through staining techniques and colony forming unit assays specific to bacteria, fungi, and algae.
JOURNAL OF CULTURAL HERITAGE
(2021)
Article
Biotechnology & Applied Microbiology
Tanja Berger, Caroline Poyntner, Rosa Margesin
Summary: The study evaluated the potential of culturable bacterial community from an Alpine coniferous forest site for degrading organic polymers and pollutants at low and moderate temperatures. The majority of the strains belonged to the phylum Proteobacteria, with differences in enzyme activities and utilization of organic compounds observed at different temperatures. The results provide insights into the impact of changing temperatures on microorganisms involved in litter degradation and nutrient turnover in Alpine forest soils.
FOLIA MICROBIOLOGICA
(2021)
Article
Microbiology
Guadalupe Pinar, Maria Carla Sclocchi, Flavia Pinzari, Piero Colaizzi, Alexandra Graf, Maria Letizia Sebastiani, Katja Sterflinger
FRONTIERS IN MICROBIOLOGY
(2020)
Article
Biology
Laura Selbmann, Zsigmond Benko, Claudia Coleine, Sybren de Hoog, Claudio Donati, Irina Druzhinina, Tamas Emri, Cassie L. Ettinger, Amy S. Gladfelter, Anna A. Gorbushina, Igor V. Grigoriev, Martin Grube, Nina Gunde-Cimerman, Zsolt Akos Karanyi, Beatrix Kocsis, Tania Kubressoian, Ida Miklos, Marton Miskei, Lucia Muggia, Trent Northen, Monika Novak-Babic, Christa Pennacchio, Walter P. Pfliegler, Istvan Pocsi, Valeria Prigione, Meritxell Riquelme, Nicola Segata, Julia Schumacher, Ekaterina Shelest, Katja Sterflinger, Donatella Tesei, Jana M. U'Ren, Giovanna C. Varese, Xabier Vazquez-Campos, Vania A. Vicente, Emanuel M. Souza, Polona Zalar, Allison K. Walker, Jason E. Stajich
Article
Biotechnology & Applied Microbiology
Rosa Margesin, Georg Volgger, Andreas O. Wagner, Dechao Zhang, Caroline Poyntner
Summary: This study found that Paraburkholderia aromaticivorans AR20-38 is capable of degrading lignin monomers at low and moderate temperatures, with the degradation of ferulic acid resulting in the stable production of high amounts of vanillic acid.
APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
(2021)
Editorial Material
Biotechnology & Applied Microbiology
Guadalupe Pinar, Katja Sterflinger
Summary: Our cultural heritage, being a common asset, requires the collaboration of diverse professionals in order to be preserved for future generations. The interdisciplinary cooperation within heritage sciences is essential for the sustainable preservation of our heritage. Advances made in conservation, restoration, and natural sciences have provided powerful tools for research and protection of historical and cultural objects.
MICROBIAL BIOTECHNOLOGY
(2021)
Article
Genetics & Heredity
Donatella Tesei, Abby J. Chiang, Markus Kalkum, Jason E. Stajich, Ganesh Babu Malli Mohan, Katja Sterflinger, Kasthuri Venkateswaran
Summary: The study found that the protein expression of black fungi differed under simulated microgravity conditions, with no significant stress response or starvation response observed. In the melanized mutant, some proteins were downregulated under microgravity conditions. No major morphological changes were observed under simulated microgravity conditions.
FRONTIERS IN GENETICS
(2021)
Letter
Allergy
Sandra Pfeiffer, Peter Sandler, Marianne Raith, Mariona Pascal, Rosa Maria Munoz-Cano, Clara San Bartolome, Katharina Noebauer, Santiago Quirce, Ebrahim Razzazi-Fazeli, Margarete Focke-Tejkl, Katja Sterflinger, Ines Swoboda
Article
Polymer Science
Valentina Pintus, Anna Piccolo, Wilfried Vetter, Ligia Maria Moretto, Katja Sterflinger, Manfred Schreiner
Summary: The ageing behavior of phenol formaldehyde (PF) foam was investigated using various analytical methods, revealing the extreme sensitivity of both open- and closed-cell PF foams to conditions typically found in indoor museums. Morphological changes, color alterations, chemical reactions, and acidity levels were all observed during the aging process.
Article
Microbiology
Caroline Poyntner, Andrea Kutzner, Rosa Margesin
Summary: Microbiota from Alpine forest soils play a vital role in carbon cycling, which can be impacted by climate change. This study evaluated culturable bacterial strains isolated from an alpine deciduous forest site for their degradation potential, with findings showing Proteobacteria phylum representatives having good biodegradation abilities at low temperatures. Additionally, 82% of strains were able to use at least one of the tested organic compounds as their sole carbon source. The presence of putative catabolic genes and gene sequencing suggested horizontal gene transfer in certain cases.
Article
Information Science & Library Science
Pascal Querner, Katja Sterflinger
Summary: The grey silverfish Ctenolepisma longicaudatum is a new and serious pest that can thrive in various buildings, causing damage to art collections and archives. Research shows that fungi living on the silverfish may pose an additional threat.
RESTAURATOR-INTERNATIONAL JOURNAL FOR THE PRESERVATION OF LIBRARY AND ARCHIVAL MATERIAL
(2021)
Article
Biotechnology & Applied Microbiology
Federica Cappa, Guadalupe Pinar, Simon Brenner, Bernadette Fruehmann, Wilfried Wetter, Manfred Schreiner, Patricia Engel, Heinz Miklas, Katja Sterflinger
Summary: This interdisciplinary research demonstrates the application of various analytical methods to study the history and conservation status of ancient manuscripts, including detecting degradation phenomena in ink materials, identifying stain components, and analyzing microbial communities. This information serves as important evidence for the preservation and risk assessment of manuscripts.
INTERNATIONAL BIODETERIORATION & BIODEGRADATION
(2022)
Article
Chemistry, Multidisciplinary
Laura Rabbachin, Guadalupe Pinar, Irit Nir, Ariel Kushmaro, Mariela J. Pavan, Elisabeth Eitenberger, Monika Waldherr, Alexandra Graf, Katja Sterflinger
Summary: This study aimed to explore the factors involved in the degradation of petroglyph sites in the Negev desert of Israel, with a particular focus on biodegradation processes. Microbiological characterization of the samples revealed the dominance of bacterial communities with resistance to radiation and desiccation. Chemical analysis identified the composition of the stone and the dark crust, and carotenoids indicative of biological colonization were found. Microscopy and analysis confirmed patterns of weathering associated with biodeteriorative microorganisms.
APPLIED SCIENCES-BASEL
(2022)
Review
Chemistry, Multidisciplinary
Guadalupe Pinar, Federica Cappa, Wilfried Vetter, Manfred Schreiner, Heinz Miklas, Katja Sterflinger
Summary: This article reviews the complementary strategies used to decipher valuable information in ancient parchment documentary materials, including molecular analysis, DNA identification, microscopical analysis, and physicochemical analysis. These methods help identify the biological origin and historical preservation of the documents without causing any harm to them.
APPLIED SCIENCES-BASEL
(2022)
