Article
Microbiology
Gamaliel Lopez-Leal, Laura Carolina Camelo-Valera, Juan Manuel Hurtado-Ramirez, Jerome Verleyen, Santiago Castillo-Ramirez, Alejandro Reyes-Munoz
Summary: This study extracted a large number of prophages from prokaryotic genomes, revealing the diversity of prophages and their relationships with their hosts. Pathogens are an important source of prophages, and the relatedness of prophages and the range of genomic hosts are influenced by the evolutionary relationships of their hosts.
Article
Ecology
Spencer Diamond, Adi Lavy, Alexander Crits-Christoph, Paula B. Matheus Carnevali, Allison Sharrar, Kenneth H. Williams, Jillian F. Banfield
Summary: Copper membrane monooxygenases (CuMMOs) are important for global carbon and nitrogen cycles. This study identified CuMMO genes in archaea outside of the Nitrososphaerales, which were classified as Ca. Angelarchaeales. The CuMMO proteins in Ca. Angelarchaeales are structurally more similar to those in Nitrososphaerales, and they also have a higher abundance of blue copper proteins and peptide/amino acid uptake and degradation capacity. These findings expand our understanding of the diversity of CuMMO enzymes in archaea.
Article
Multidisciplinary Sciences
Ebru Destan, Busra Yuksel, Bradley B. Tolar, Esra Ayan, Sam Deutsch, Yasuo Yoshikuni, Soichi Wakatsuki, Christopher A. Francis, Hasan DeMirci
Summary: The protein encoded by Nmar_1308 plays a crucial role in the ammonia-oxidizing thaumarchaeal 3HP/4HB cycle by acting as both CCAH and 3HPD, thereby reducing the number of enzymes required for CO2 fixation and lowering the overall cost of biosynthesis. The high-resolution crystal structure of this bifunctional enzyme provides insights into key catalytic residues in the thaumarchaeal 3HP/4HB pathway.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Patrick Schultheiss, Sabine S. Nooten, Runxi Wang, Mark K. L. Wong, Francois Brassard, Benoit Guenard
Summary: Knowledge on the distribution and abundance of organisms is essential. However, there is currently a lack of such knowledge for insects, particularly ants. This study provides an empirical estimate of global ant abundance based on 489 studies, highlighting their significant role in terrestrial ecosystems and the gaps in our knowledge.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Review
Food Science & Technology
Sima Ghaffari, Amin Abbasi, Mohammad Hossein Somi, Seyed Yaghoub Moaddab, Leila Nikniaz, Hossein Samadi Kafil, Hamed Ebrahimzadeh Leylabadlo
Summary: This article comprehensively reviews the features of Akkermansia muciniphila in terms of its function in host physiology and frequently utilized nutrition, indicating its potential as next-generation probiotics. However, certain issues need to be addressed before its extensive use as a probiotic.
CRITICAL REVIEWS IN FOOD SCIENCE AND NUTRITION
(2023)
Article
Environmental Sciences
Mutong Niu, Feng Zhou, Yi Yang, Ye Sun, Tianle Zhu, Fangxia Shen
Summary: This study investigated the characteristics of airborne archaea in Beijing during springtime, revealing soil as the primary source for releasing archaea into the environment. It was found that air quality and sandstorms can impact the abundance of airborne archaea, and dispersal-related neutral processes play a crucial role in shaping the structure of the archaeal assembly.
SCIENCE OF THE TOTAL ENVIRONMENT
(2021)
Article
Biology
Aspen T. Reese, Katia S. Chadaideh, Caroline E. Diggins, Laura D. Schell, Mark Beckel, Peggy Callahan, Roberta Ryan, Melissa Emery Thompson, Rachel N. Carmody
Summary: The study found that domestication and industrialization have had similar impacts on gut microbiota, mainly through changes in diet and ecological environment. Successfully re-establishing wild-like microbiota in domesticated mice through experiments demonstrates the potential for reshaping gut microbiota in domesticated animals.
Article
Ecology
Emilie Lyautey, Elodie Billard, Nathalie Tissot, Stephan Jacquet, Isabelle Domaizon
Summary: This study investigated the spatial variability and temporal dynamics of methanogenic Archaea and methanotrophic bacteria in Lake Bourget, France. Changes in both structure and abundance were detected mainly at the water-sediment interface in relation to the lake seasonal oxygenation dynamics.
Article
Spectroscopy
Dongdong Ni, Heather E. Smyth, Michael J. Gidley, Daniel Cozzolino
Summary: This study evaluated the ability of a portable NIR instrument to analyze different tissues in healthy individuals and correlate spectral data with age, RMR, RQ, BF, and BMI. The results suggest that non-destructive techniques like vibrational spectroscopy have the potential to better categorize and understand individual differences in physiology and nutrition.
SPECTROCHIMICA ACTA PART A-MOLECULAR AND BIOMOLECULAR SPECTROSCOPY
(2022)
Article
Biology
Alexander Y. Merkel, Nikolay A. Chernyh, Nikolai V. Pimenov, Elizaveta A. Bonch-Osmolovskaya, Alexander I. Slobodkin
Summary: This study investigated the phylogenetic composition and metabolic potential of prokaryotic communities in terrestrial mud volcanoes in Russia's Taman Peninsula using a metagenomic approach. A unique community containing a high abundance of ANME-3 archaea was discovered, indicating their capability of anaerobic methane oxidation. Metagenome-assembled genomes of archaeal and bacterial members were analyzed, revealing the presence of genes for methanogenesis in ANME-3 archaea and suggesting their ability to couple methane oxidation with the reduction of metal oxides or interspecies electron transfer.
Review
Physiology
Nazli Karimi
Summary: Skin aging is a complex process influenced by various factors, and maintaining skin health is important for overall well-being. There is a growing demand for anti-aging products and treatments, but limitations exist in terms of safety and effectiveness. Researchers are now exploring safer and more physiological approaches, such as dietary changes, synchronized topical treatments, and utilization of endogenous compounds, to combat skin aging.
FRONTIERS IN PHYSIOLOGY
(2023)
Article
Environmental Sciences
Jianqiang Zhu, Xiaowei Dong, Nan Zhao, Shengtao Jiang, Hangbiao Jin
Summary: This study analyzed microplastic pollution in 354 samples of polystyrene-made food containers (PMFCs) collected from different restaurants in 28 Chinese cities. Microplastics were detected in all samples, with an abundance ranging from 5 to 173 items per container. The highest mean abundance of microplastics was found in PMFC samples from Taiyuan (86 items/container), while lower abundances were observed in samples from Urumqi (19 items/container) and Fuzhou (18 items/container). Fiber was the predominant shape of microplastics in most samples, and the major polymer composition was polystyrene, accounting for 45-90% of total polymers. The estimated oral exposure of microplastics for the general population in different Chinese cities ranged from 0.24 to 1.4 items/kg bw/day. These findings are important for assessing human exposure risk and understanding the sources of microplastic contamination.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Review
Marine & Freshwater Biology
Cui-Jing Zhang, Yu-Lian Chen, Yi-Hua Sun, Jie Pan, Ming-Wei Cai, Meng Li
Summary: Archaea in mangroves play essential roles in biogeochemical cycles and are crucial for carbon, nitrogen, and sulfur cycling. Innovative cultivation strategies, such as single-cell isolation and high-throughput culturing, provide more opportunities to study previously uncultured archaeal lineages in mangrove wetlands.
MARINE LIFE SCIENCE & TECHNOLOGY
(2021)
Article
Immunology
Justyna Mika, Kengo Yoshida, Yoichiro Kusunoki, Serge M. Candeias, Joanna Polanska
Summary: Peripheral T lymphocyte proliferation is partly dependent on their thymic developmental history. The rate of proliferation of T cells with different TRB rearrangement status is different in men and women before the age of 18, but similar thereafter. Over time, T cell clone size becomes more heterogeneous, and in adults, it is always more even in women. A longitudinal analysis of TRB repertoires obtained at ten-year intervals from individual men and women confirms the findings of this cross-sectional study.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Motonori Kurosumi, Koji Mizukoshi, Maya Hongo, Miyuki G. Kamachi
Summary: Most aging research focuses on the frontal face and ignores the importance of observing facial features from different angles. This study investigates the effect of facial observation angles on age impression and finds that different angles can affect how old a person appears, especially when observing the face from the side.
Article
Microbiology
Cynthia Maria Chibani, Alexander Mahnert, Guillaume Borrel, Alexandre Almeida, Almut Werner, Jean-Francois Brugere, Simonetta Gribaldo, Robert D. Finn, Ruth A. Schmitz, Christine Moissl-Eichinger
Summary: The study analyzed 1,167 nonredundant archaeal genomes from human gut microbiomes, revealing previously undescribed genera, associations with sociodemographic factors, and the presence of an archaeal virome. The research demonstrates that archaea exhibit specific genomic and functional adaptations to the host, carrying a complex virome that plays a role in human physiology. This work expands our understanding of the human archaeome and provides a genome catalogue for future studies.
NATURE MICROBIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Janina Rahlff, Till L. Bornemann, Anna Lopatina, Konstantin Severinov, Alexander J. Probst
Summary: Extreme Antarctic conditions serve as a close analogue of extraterrestrial environments. Tracking genetic signatures of host-associated bacteriophages across the Antarctic continent helps understand viral dispersal over long distances, highlighting the potential for microbial dispersal in harsh environments. The discovery of highly identical phage genome fragments in snow samples and seawater from distant locations points to the wide dispersal of these genetic elements, with implications for planetary protection in astrobiology.
APPLIED AND ENVIRONMENTAL MICROBIOLOGY
(2022)
Article
Biology
Benjamin H. Meyer, Panagiotis S. Adam, Ben A. Wagstaff, George E. Kolyfetis, Alexander J. Probst, Sonja Albers, Helge C. Dorfmueller, Philip A. Cole
Summary: Protein N-glycosylation is a post-translational modification that occurs in organisms across different domains of life, including crenarchaeal. The identification of the archaeal glycosylation enzyme 24 (Agl24) in thermostable archaeal beta-1,4-N-acetylglucosaminyltransferase provides insights into the synthesis of the N-glycan chitobiose core and its functional importance. Phylogenetic analysis reveals similarities between Agl24 and eukaryotic and bacterial homologs, indicating a potential evolutionary relationship.
Correction
Microbiology
Indra Monsees, Victoria Turzynski, Sarah P. Esser, Andre Soares, Lara I. Timmermann, Katrin Weidenbach, Jarno Banas, Michael Kloster, Bank Beszteri, Ruth A. Schmitz, Alexander J. Probst
Article
Environmental Sciences
Otavio H. B. Pinto, Till L. V. Bornemann, Rafael S. Oliveira, Tayna D. Frederico, Betania F. Quirino, Alexander J. Probst, Mayanne A. M. de Freitas, Fabiano L. Thompson, Ricardo H. Kruger
Summary: The symbiotic relationship between coral and photosynthetic microorganisms is crucial for coral reef existence. However, little is known about the function of the microbiome associated with sponges, which are the major epifauna of the Great Amazon Reef System (GARS). This study used genome-resolved metagenomics to investigate how the microbiome of sponges supports its host and overcomes the reduced light availability. The findings suggest that the sponge microbiome mainly relies on plume-associated organic carbon and its heterotrophic microbiota.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Geosciences, Multidisciplinary
Will A. Overholt, Susan Trumbore, Xiaomei Xu, Till L. Bornemann, Alexander J. Probst, Markus Krueger, Martina Herrmann, Bo Thamdrup, Laura A. Bristow, Martin Taubert, Valerie F. Schwab, Martin Hoelzer, Manja Marz, Kirsten Kuesel
Summary: The terrestrial subsurface contains most freshwater reserves and prokaryotic biomass. A study estimated carbon fixation rates in a carbonate aquifer using a C-14-labelling technique and found similarities to those in oligotrophic marine surface waters. The study suggests the importance of in situ carbon fixation in subsurface ecosystem processes.
Article
Biotechnology & Applied Microbiology
William B. Whitman, Maria Chuvochina, Brian P. Hedlund, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain Sutcliffe, Stephanus N. Venter
Summary: Genomics has been fully integrated into prokaryotic systematics over the past fifteen years. The SeqCode has been developed to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types, simplifying nomenclature and promoting synergies between different disciplines.
SYSTEMATIC AND APPLIED MICROBIOLOGY
(2022)
Article
Microbiology
Brian P. Hedlund, Maria Chuvochina, Philip Hugenholtz, Konstantinos T. Konstantinidis, Alison E. Murray, Marike Palmer, Donovan H. Parks, Alexander J. Probst, Anna-Louise Reysenbach, Luis M. Rodriguez-R, Ramon Rossello-Mora, Iain C. Sutcliffe, Stephanus N. Venter, William B. Whitman
Summary: The SeqCode is a new nomenclature system for prokaryotes that allows naming of organisms based on their genome sequences. It operates similarly to the International Code of Nomenclature of Prokaryotes (ICNP) but uses the SeqCode Registry for registration, validation, and linking of names and metadata. This system provides a reproducible and objective framework for naming prokaryotes regardless of cultivability.
NATURE MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Panagiotis S. Adam, George E. Kolyfetis, Till L. V. Bornemann, Constantinos E. Vorgias, Alexander J. Probst
Summary: The study reveals that anaerobic methane metabolism is a characteristic of Archaea, and the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen. The research also highlights that methyl-dependent hydrogenotrophic methanogenesis has emerged independently multiple times. The remnants of methanogenesis play a crucial role in carbon cycling in anoxic environments.
Article
Gastroenterology & Hepatology
Marcus Blohs, Alexander Mahnert, Kevin Brunnader, Christina Flucher, Christoph Castellani, Holger Till, Georg Singer, Christine Moissl-Eichinger
Summary: Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. In this study, the microbiome of samples from 60 children and adolescents with AA was investigated to assess the composition and potential function of bacteria, archaea, and fungi. The analysis revealed a shift in the microbiome depending on the severity of AA, with complicated cases associated with oral bacterial pathogens and uncomplicated cases characterized by gut-associated microbiomes. Advanced microbiome diagnosis could improve the non-surgical treatment of uncomplicated AA.
Article
Microbiology
Till L. V. Bornemann, Sarah P. Esser, Tom L. Stach, Tim Burg, Alexander J. Probst
Summary: uBin is a GUI-based standalone software for bin refinement, which improves the quality of bacterial and archaeal genomes from metagenomes by using GC content, coverage, and taxonomy. It has shown success in improving 78.9% of bins by reducing contamination when applied to the public CAMI dataset. It can also be used as a standalone binner for metagenomes from the International Space Station, revealing the active proliferation of microbes in Earth's lower orbit. uBin is easy to install and can be used for binning, communicating metagenomic results, and education purposes. The software and its helper scripts are open source and available online.
ENVIRONMENTAL MICROBIOLOGY
(2023)
Article
Virology
Victoria Turzynski, Lea Griesdorn, Cristina Moraru, Andre R. Soares, Sophie A. A. Simon, Tom L. L. Stach, Janina Rahlff, Sarah P. P. Esser, Alexander J. J. Probst
Summary: The spatial and temporal distribution of lytic viruses in deep groundwater has not been explored yet. In this study, we investigate viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a four-year period. By using virus-targeted direct-geneFISH (virusFISH), we observe a significant and steady increase in virus infections from 2019 to 2022. Our findings also reveal different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection in deep groundwater. The stable virus-host interaction observed in these samples suggests that the uncultivated virus-host system described here could serve as a suitable model for studying deep biosphere virus-host interactions in future research endeavors.
Review
Physics, Applied
Elizabeth A. Holman, Harinarayan Krishnan, Derek R. Holman, Hoi-Ying N. Holman, Paul W. Sternberg
Summary: Autonomous experimentation is a growing field of research that focuses on autonomous vehicles, combinatorial discovery in materials science and drug discovery, and iterative research loops. However, applying autonomous approaches to high-dimensional mapping technologies like scanning hyperspectral imaging of biological systems is challenging due to sample complexity and heterogeneity. This article explores adaptive sampling algorithms and surrogate modeling to define autonomous adaptive data acquisition as a flexible building block for future biological imaging experimentation. It discusses recent implementations of autonomous adaptive data acquisition for scanning hyperspectral imaging, emphasizes the design variation from a goal-oriented perspective, and presents a modular architecture to address time resolution challenges in high-dimensional scanning hyperspectral imaging of nonequilibrium dynamical systems.
APPLIED PHYSICS REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Eva-Maria Pferschy-Wenzig, Olaf Kunert, Timo Thumann, Christine Moissl-Eichinger, Rudolf Bauer
Summary: Silymarin, a mixture of flavonolignans from milk thistle fruits, has various pharmacological activities. However, its oral bioavailability is limited due to low water solubility and extensive metabolism. The study investigated the biotransformation of silymarin by gut microorganisms and identified multiple metabolites, including demethylation products and low molecular weight aromatic metabolites. The potential pharmacological activities of these gut microbial metabolites warrant further examination.
Article
Multidisciplinary Sciences
Janina Rahlff, Sarah P. Esser, Julia Plewka, Mara Elena Heinrichs, Andre Soares, Claudio Scarchilli, Paolo Grigioni, Heike Wex, Helge-Ansgar Giebel, Alexander J. Probst
Summary: Marine viruses can be dispersed into the atmosphere through the air-sea interface and detected in rainwater. Virus enrichment in the surface microlayer and sea foams, as well as higher G/C base content in viruses from rain and aerosols, were observed. These findings support the transmission of viruses along the water cycle.
NATURE COMMUNICATIONS
(2023)