Preprints
Preprints of key researchers of our CoE – since 2024
Hu, Huifeng; Karwautz, Clemens; Duszka, Kalina; Karner, Thomas; Wagner, Isabella; Grander, Christoph; Grander, Wilhelm; Steinwidder, Laura; Boito, Lucilla; de Velde, Viktor Van; Bauters, Marijn; Boeckx, Pascal; Seki, David; Glasl, Bettina; Thiele, Stefan; Schmidt, Hannes; Seneca, Joana; Wagner, Michael; Pjevac, Petra
bioRxiv, 2025.
@unpublished{Hu2025,
title = {Revised 16S rRNA V4 hypervariable region targeting primers enhance detection of Patescibacteria and other lineages across diverse environments},
author = {Huifeng Hu and Clemens Karwautz and Kalina Duszka and Thomas Karner and Isabella Wagner and Christoph Grander and Wilhelm Grander and Laura Steinwidder and Lucilla Boito and Viktor Van de Velde and Marijn Bauters and Pascal Boeckx and David Seki and Bettina Glasl and Stefan Thiele and Hannes Schmidt and Joana Seneca and Michael Wagner and Petra Pjevac},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.11.26.690684},
doi = {10.1101/2025.11.26.690684},
year = {2025},
date = {2025-11-26},
urldate = {2025-11-26},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:p>Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexota and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:p>Primer bias in 16S rRNA gene amplicon sequencing can distort microbial diversity estimates by underrepresenting key taxa. We introduce a modified primer pair (V4-EXT) targeting the hypervariable V4 region of bacterial and archaeal 16S rRNA genes, with improved in silico taxonomic inclusivity. To benchmark performance, we analyzed 938 samples from terrestrial, aquatic, and host-associated habitats, comparing microbial community profiles derived with V4-EXT and the currently most widely used V4-targeted primers. V4-EXT substantially improved the detection of Patescibacteria and other underrepresented lineages, such as Chloroflexota and Iainarchaeota, while enhancing recovery of novel amplicon sequence variants across sample types. Overall, V4-EXT provides broader taxonomic coverage and more inclusive microbial community profiles, particularly in high-diversity ecosystems such as groundwater and soils. We propose V4-EXT as a robust successor for comprehensive microbial community analysis across diverse habitats.</jats:p>
Jelusic, Barbara; Boerno, Stefan; Schimmel, Patrick; Wurm, Philipp; Przysiecki, Nicole; Watschinger, Christina; Wolfgruber, Stella; Hardt, Melina; Anthofer, Margit; Ehmann, Sandra; Klages, Sven; Zatloukal, Kurt; Timmermann, Bernd; Moschen, Alexander; Gorkiewicz, Gregor
Research Square, 2025.
@unpublished{Jelusic2025,
title = {Reduced SARS-CoV-2 infection levels and pathotype specific altered antiviral transcriptional response in IBD intestinal organoids},
author = {Barbara Jelusic and Stefan Boerno and Patrick Schimmel and Philipp Wurm and Nicole Przysiecki and Christina Watschinger and Stella Wolfgruber and Melina Hardt and Margit Anthofer and Sandra Ehmann and Sven Klages and Kurt Zatloukal and Bernd Timmermann and Alexander Moschen and Gregor Gorkiewicz},
url = {https://www.researchsquare.com/article/rs-8029502/v1},
doi = {10.21203/rs.3.rs-8029502/v1},
year = {2025},
date = {2025-11-26},
urldate = {2025-11-26},
publisher = {Springer Science and Business Media LLC},
abstract = {<title>Abstract</title>
<p>
Background
IBD is characterized by altered immune reactions and infections are thought to trigger chronic inflammation in IBD. The gut represents a productive reservoir for SARS-CoV-2 and the aforementioned factors together with immunosuppression used to treat IBD are likely influencing the outcomes of IBD patients with COVID-19.
Methods
We used large and small intestinal organoids from ulcerative colitis and Crohn's disease patients and controls to comparatively assess infection levels and transcriptional response of the gut epithelium during SARS-CoV-2 infection.
Results
Our analysis showed that IBD epithelia exhibit reduced viral loads compared to controls associated with a reduced expression of SARS-CoV-2 entry factors including the host receptor ACE2. Moreover, several genes implicated in the epithelial response to viral infection are intrinsically altered in IBD potentially counteracting viral propagation. Notably, differences between IBD phenotypes exist wherein ulcerative colitis represents with induced cell death pathways and increased
<italic>IL1B</italic>
expression despite lower viral loads suggestive of increased epithelial stress.
Conclusions
Altogether our analysis shows that the IBD epithelium is not more prone to SARS-CoV-2 infection and that several antiviral response genes are intrinsically activated in IBD. Moreover, ulcerative colitis and Crohn's disease exhibit specific transcriptional differences which might explain the differing COVID-19 outcomes between IBD phenotypes.
</p>},
howpublished = {Research Square},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<title>Abstract</title>
<p>
Background
IBD is characterized by altered immune reactions and infections are thought to trigger chronic inflammation in IBD. The gut represents a productive reservoir for SARS-CoV-2 and the aforementioned factors together with immunosuppression used to treat IBD are likely influencing the outcomes of IBD patients with COVID-19.
Methods
We used large and small intestinal organoids from ulcerative colitis and Crohn's disease patients and controls to comparatively assess infection levels and transcriptional response of the gut epithelium during SARS-CoV-2 infection.
Results
Our analysis showed that IBD epithelia exhibit reduced viral loads compared to controls associated with a reduced expression of SARS-CoV-2 entry factors including the host receptor ACE2. Moreover, several genes implicated in the epithelial response to viral infection are intrinsically altered in IBD potentially counteracting viral propagation. Notably, differences between IBD phenotypes exist wherein ulcerative colitis represents with induced cell death pathways and increased
<italic>IL1B</italic>
expression despite lower viral loads suggestive of increased epithelial stress.
Conclusions
Altogether our analysis shows that the IBD epithelium is not more prone to SARS-CoV-2 infection and that several antiviral response genes are intrinsically activated in IBD. Moreover, ulcerative colitis and Crohn's disease exhibit specific transcriptional differences which might explain the differing COVID-19 outcomes between IBD phenotypes.
</p>
<p>
Background
IBD is characterized by altered immune reactions and infections are thought to trigger chronic inflammation in IBD. The gut represents a productive reservoir for SARS-CoV-2 and the aforementioned factors together with immunosuppression used to treat IBD are likely influencing the outcomes of IBD patients with COVID-19.
Methods
We used large and small intestinal organoids from ulcerative colitis and Crohn's disease patients and controls to comparatively assess infection levels and transcriptional response of the gut epithelium during SARS-CoV-2 infection.
Results
Our analysis showed that IBD epithelia exhibit reduced viral loads compared to controls associated with a reduced expression of SARS-CoV-2 entry factors including the host receptor ACE2. Moreover, several genes implicated in the epithelial response to viral infection are intrinsically altered in IBD potentially counteracting viral propagation. Notably, differences between IBD phenotypes exist wherein ulcerative colitis represents with induced cell death pathways and increased
<italic>IL1B</italic>
expression despite lower viral loads suggestive of increased epithelial stress.
Conclusions
Altogether our analysis shows that the IBD epithelium is not more prone to SARS-CoV-2 infection and that several antiviral response genes are intrinsically activated in IBD. Moreover, ulcerative colitis and Crohn's disease exhibit specific transcriptional differences which might explain the differing COVID-19 outcomes between IBD phenotypes.
</p>
Glasl, Bettina; Kitzinger, Katharina; Luter, Heidi M.; Legin, Anton; Salas, Erika; Heldwein, Nathalie; Damjanovic, Katarina; Schuster, Stefan; Rutsch, Marie; Vekeman, Bram; Speth, Daan R; Geerlings, Nicole MJ; Pjevac, Petra; Séneca, Joana; Watzka, Margarete; Wanek, Wolfgang; Wagner, Michael
Branched-chain amino acid assimilation promotes mixotrophy of ammonia-oxidizing archaeal sponge symbionts Unpublished
bioRxiv, 2025.
@unpublished{Glasl2025,
title = {Branched-chain amino acid assimilation promotes mixotrophy of ammonia-oxidizing archaeal sponge symbionts},
author = {Bettina Glasl and Katharina Kitzinger and Heidi M. Luter and Anton Legin and Erika Salas and Nathalie Heldwein and Katarina Damjanovic and Stefan Schuster and Marie Rutsch and Bram Vekeman and Daan R Speth and Nicole MJ Geerlings and Petra Pjevac and Joana Séneca and Margarete Watzka and Wolfgang Wanek and Michael Wagner},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.09.09.672702},
doi = {10.1101/2025.09.09.672702},
year = {2025},
date = {2025-09-09},
urldate = {2025-09-09},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:p>Ammonia-oxidizing archaea (AOA) frequently form symbiotic associations with marine sponges. While free-living AOA are generally considered metabolically constrained chemolithoautotrophs, sponge-associated AOA encode for a branched-chain amino acid (BCAA) transporter, suggesting mixotrophic potential. Here, we test the unusual mixotrophic lifestyle of sponge-associated AOA by tracing the assimilation of <jats:sup>13</jats:sup>C- and <jats:sup>15</jats:sup>N-labeled BCAA in the sponge holobiont Ianthella basta. We demonstrate that BCAA degradation fuels ammonia oxidation and quantify BCAA uptake at the single-cell level by combining stable isotope probing, catalyzed reporter deposition fluorescence <jats:italic>in situ</jats:italic> hybridization, and nanoscale secondary ion mass spectrometry. Our results reveal that sponge-associated AOA are mixotrophic, assimilating BCAA as an additional carbon and nitrogen source. This metabolic adaptation may modulate BCAA availability in the holobiont, potentially regulating the host's mTOR pathway. Collectively, our study reveals a novel nutritional interaction in sponge holobionts and challenges the perception of constrained metabolic capacities of AOA.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:p>Ammonia-oxidizing archaea (AOA) frequently form symbiotic associations with marine sponges. While free-living AOA are generally considered metabolically constrained chemolithoautotrophs, sponge-associated AOA encode for a branched-chain amino acid (BCAA) transporter, suggesting mixotrophic potential. Here, we test the unusual mixotrophic lifestyle of sponge-associated AOA by tracing the assimilation of <jats:sup>13</jats:sup>C- and <jats:sup>15</jats:sup>N-labeled BCAA in the sponge holobiont Ianthella basta. We demonstrate that BCAA degradation fuels ammonia oxidation and quantify BCAA uptake at the single-cell level by combining stable isotope probing, catalyzed reporter deposition fluorescence <jats:italic>in situ</jats:italic> hybridization, and nanoscale secondary ion mass spectrometry. Our results reveal that sponge-associated AOA are mixotrophic, assimilating BCAA as an additional carbon and nitrogen source. This metabolic adaptation may modulate BCAA availability in the holobiont, potentially regulating the host's mTOR pathway. Collectively, our study reveals a novel nutritional interaction in sponge holobionts and challenges the perception of constrained metabolic capacities of AOA.</jats:p>
Lee, Ui-Ju; Gwak, Joo-Han; Abiola, Christiana; Lee, Seongjun; Yu, Jin-Sun; Si, Ok-Ja; Cho, Hyo Je; Quan, Zhe-Xue; Kitzinger, Katharina; Daims, Holger; Wagner, Michael; Jung, Man-Young; Rhee, Sung-Keun
Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase Unpublished
bioRxiv, 2025.
@unpublished{Lee2025b,
title = {Kinetic Plasticity of Nitrite-Oxidizing Bacteria Containing Cytoplasmic Nitrite Oxidoreductase},
author = {Ui-Ju Lee and Joo-Han Gwak and Christiana Abiola and Seongjun Lee and Jin-Sun Yu and Ok-Ja Si and Hyo Je Cho and Zhe-Xue Quan and Katharina Kitzinger and Holger Daims and Michael Wagner and Man-Young Jung and Sung-Keun Rhee},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.07.31.663499},
doi = {10.1101/2025.07.31.663499},
year = {2025},
date = {2025-07-22},
urldate = {2025-07-31},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Abstract</jats:title>
<jats:p>Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. <jats:italic>Nitrobacter winogradskyi</jats:italic> Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent <jats:italic>K</jats:italic>
<jats:sub>m</jats:sub> (25.9 μM) and a high specific affinity <jats:italic>a°</jats:italic> (440.5 l g cells<jats:sup>−1</jats:sup> h<jats:sup>−1</jats:sup>), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that <jats:italic>Nitrobacter</jats:italic> can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both <jats:italic>r</jats:italic>-and <jats:italic>K</jats:italic>-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Abstract</jats:title>
<jats:p>Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. <jats:italic>Nitrobacter winogradskyi</jats:italic> Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent <jats:italic>K</jats:italic>
<jats:sub>m</jats:sub> (25.9 μM) and a high specific affinity <jats:italic>a°</jats:italic> (440.5 l g cells<jats:sup>−1</jats:sup> h<jats:sup>−1</jats:sup>), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that <jats:italic>Nitrobacter</jats:italic> can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both <jats:italic>r</jats:italic>-and <jats:italic>K</jats:italic>-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.</jats:p>
<jats:p>Nitrite oxidation, the second step of nitrification, is essential to the global nitrogen cycle. Nitrite-oxidizing bacteria (NOB) are classified into two groups based on the cellular localization of their key enzyme nitrite oxidoreductase (NXR): periplasmic (pNXR) and cytoplasmic (cNXR). The use of a cNXR by NOB has been reported to be linked to a lower nitrite affinity and energy efficiency of nitrite oxidation, indicating adaptation to nitrogen-rich environments. In this study, cNXR NOB model strains demonstrated nitrite concentration-dependent shifts in optimal growth pH, a behavior not observed in pNXR NOB. <jats:italic>Nitrobacter winogradskyi</jats:italic> Nb-255 (cNXR NOB), grown at 1 mM nitrite (pH 7.5), exhibited a high nitrite affinity in terms of apparent <jats:italic>K</jats:italic>
<jats:sub>m</jats:sub> (25.9 μM) and a high specific affinity <jats:italic>a°</jats:italic> (440.5 l g cells<jats:sup>−1</jats:sup> h<jats:sup>−1</jats:sup>), both comparable to pNXR NOB in microrespirometry-based kinetic assays. Unexpectedly, cells pre-grown at 10 mM nitrite (pH 7.5) achieved a pNXR-like affinity at pH 5.5 without prior adaptation to acidic conditions. In contrast, pNXR NOB exhibited consistent kinetic behavior across different pH conditions. Kinetic inhibition in the presence of nitrate suggested that this plasticity is driven by a regulated interplay between nitrite uniport and nitrite/nitrate antiporter systems. Our findings indicate that <jats:italic>Nitrobacter</jats:italic> can dynamically modulate nitrite affinity in response to both nitrite concentration and pH, conferring a flexible adaptation strategy that features traits of both <jats:italic>r</jats:italic>-and <jats:italic>K</jats:italic>-strategists across a range of environmental conditions. This adaptive plasticity likely extends to other cNXR-containing NOB in response to fluctuating environmental conditions.</jats:p>
Gwak, Joo-Han; Olabisi, Adebisi; Lee, Ui-Ju; Abiola, Christiana; Lee, Seongjun; Do, Hackwon; Choi, Yun Ji; Lee, Jay-Jung; Jung, Man-Young; Jehmlich, Nico; Bergen, Martin; Wagner, Michael; Awala, Samuel Imisi; Quan, Zhe-Xue; Rhee, Sung-Keun
Hypoosmolarity inhibits archaeal ammonia oxidation Unpublished
bioRxiv, 2025.
@unpublished{Gwak2025,
title = {Hypoosmolarity inhibits archaeal ammonia oxidation},
author = {Joo-Han Gwak and Adebisi Olabisi and Ui-Ju Lee and Christiana Abiola and Seongjun Lee and Hackwon Do and Yun Ji Choi and Jay-Jung Lee and Man-Young Jung and Nico Jehmlich and Martin Bergen and Michael Wagner and Samuel Imisi Awala and Zhe-Xue Quan and Sung-Keun Rhee},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.07.07.663500},
doi = {10.1101/2025.07.07.663500},
year = {2025},
date = {2025-07-07},
urldate = {2025-07-07},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Abstract</jats:title>
<jats:p>Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (∼120 μS/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by <jats:italic>Nitrosomonas oligotropha</jats:italic>, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by “<jats:italic>Ca.</jats:italic> Nitrosotenuis” of the <jats:italic>Nitrosopumilaceae</jats:italic> family, was stimulated by high salinity (∼760 μS/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by <jats:italic>N. oligotropha,</jats:italic> significantly increased under both low (∼170 μS/cm) and high salinity (∼850 μS/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of <jats:italic>Nitrosopumilaceae</jats:italic>, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Abstract</jats:title>
<jats:p>Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (∼120 μS/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by <jats:italic>Nitrosomonas oligotropha</jats:italic>, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by “<jats:italic>Ca.</jats:italic> Nitrosotenuis” of the <jats:italic>Nitrosopumilaceae</jats:italic> family, was stimulated by high salinity (∼760 μS/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by <jats:italic>N. oligotropha,</jats:italic> significantly increased under both low (∼170 μS/cm) and high salinity (∼850 μS/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of <jats:italic>Nitrosopumilaceae</jats:italic>, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.</jats:p>
<jats:p>Salinity strongly influences the physiology and distribution of nitrifying microorganisms, yet the effects of low salinity on them remain understudied. This study investigates the impact of hypoosmolarity on different groups of ammonia oxidizers in soil and lake environments, as well as in pure culture isolates. In soil microcosms amended with ammonium, at low salinity levels (∼120 μS/cm), comparable to values commonly found in pristine terrestrial and aquatic environments, the abundance of ammonia-oxidizing bacteria (AOB), dominated by <jats:italic>Nitrosomonas oligotropha</jats:italic>, significantly increased. In contrast, the growth of ammonia-oxidizing archaea (AOA), dominated by “<jats:italic>Ca.</jats:italic> Nitrosotenuis” of the <jats:italic>Nitrosopumilaceae</jats:italic> family, was stimulated by high salinity (∼760 μS/cm). In ammonium-fed lake microcosms, the abundance of AOB, dominated by <jats:italic>N. oligotropha,</jats:italic> significantly increased under both low (∼170 μS/cm) and high salinity (∼850 μS/cm) conditions. In the presence of allylthiourea, a bacterial nitrification inhibitor, AOA were sensitive to low salinity in both soil and lake microcosms. Consistently, pure culture studies revealed marked growth inhibition of AOA, especially members of <jats:italic>Nitrosopumilaceae</jats:italic>, under hypoosmolarity, unlike AOB and complete ammonia oxidizer (comammox) strains. Comparative genomic analyses with AOB and comammox, along with transcriptomic studies, suggested that the sensitivity of AOA to hypoosmolarity stress was possibly due to a lack of sophisticated osmoregulatory transport systems and their S-layer cell wall structure. Overall, this study highlights hypoosmolarity as a key factor shaping the ecological niches and distribution of ammonia oxidizers, as well as nitrification activities, in terrestrial and aquatic environments that are increasingly affected by intensified water cycles due to climate change.</jats:p>
Mohammadzadeh, Rokhsareh; Mahnert, Alexander; Zurabischvili, Tamara; Wink, Lisa; Kumpitsch, Christina; Habisch, Hansjoerg; Sprengel, Jannik; Filek, Klara; Mertelj, Polona; Pernitsch, Dominique; Hingerl, Kerstin; Gorkiewicz, Gregor; Diener, Christian; Loy, Alexander; Kolb, Dagmar; Trautwein, Christoph; Madl, Tobias; Moissl-Eichinger, Christine
bioRxiv, 2025.
@unpublished{Mohammadzadeh2025b,
title = {textitMethanobrevibacter smithiiassociates with colorectal cancer through trophic control of the cancer bacteriome},
author = {Rokhsareh Mohammadzadeh and Alexander Mahnert and Tamara Zurabischvili and Lisa Wink and Christina Kumpitsch and Hansjoerg Habisch and Jannik Sprengel and Klara Filek and Polona Mertelj and Dominique Pernitsch and Kerstin Hingerl and Gregor Gorkiewicz and Christian Diener and Alexander Loy and Dagmar Kolb and Christoph Trautwein and Tobias Madl and Christine Moissl-Eichinger},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.06.12.659283},
doi = {10.1101/2025.06.12.659283},
year = {2025},
date = {2025-06-12},
urldate = {2025-06-12},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Summary</jats:title><jats:p>The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea in human disease remains elusive. Here we searched for gut archaeal signatures of disease by screening 19 cross-sectional clinical studies comprising more than 1,800 individuals. We found that associations between Archaea and medical disorders are common but highly variable and are dominated by a significant increase of<jats:italic>Methanobrevibacter smithii</jats:italic>in colorectal cancer (CRC) patients. Metabolic modelling and<jats:italic>in vitro</jats:italic>co-culture identified distinct mutualistic interactions of<jats:italic>M. smithii</jats:italic>with CRC-causing bacteria such as<jats:italic>Fusobacterium nucleatum</jats:italic>, including metabolic enhancement. Metabolomics further revealed archaeal-derived compounds with tumor-modulating properties. This provides the first mechanistic link between human gut archaeome and CRC and highlights its role in modulating health in humans through trophic control of the resident bacteriome.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Summary</jats:title><jats:p>The human gut is colonized by trillions of microbes that influence the health of their human host. Whereas many bacterial species have now been linked to a variety of different diseases, the involvement of Archaea in human disease remains elusive. Here we searched for gut archaeal signatures of disease by screening 19 cross-sectional clinical studies comprising more than 1,800 individuals. We found that associations between Archaea and medical disorders are common but highly variable and are dominated by a significant increase of<jats:italic>Methanobrevibacter smithii</jats:italic>in colorectal cancer (CRC) patients. Metabolic modelling and<jats:italic>in vitro</jats:italic>co-culture identified distinct mutualistic interactions of<jats:italic>M. smithii</jats:italic>with CRC-causing bacteria such as<jats:italic>Fusobacterium nucleatum</jats:italic>, including metabolic enhancement. Metabolomics further revealed archaeal-derived compounds with tumor-modulating properties. This provides the first mechanistic link between human gut archaeome and CRC and highlights its role in modulating health in humans through trophic control of the resident bacteriome.</jats:p>
Krasenbrink, Julia; Chen, Song-Can; Tanabe, Tomohisa Sebastian; Sarikece, Huseyin; Meurs, Pleun; Borusak, Sabrina; Samrat, Rahul; Osvatic, Jay; Seneca, Joana; Hausmann, Bela; Speth, Daan R; Selberherr, Evelyne; Wanek, Wolfgang; Schleheck, David; Mussmann, Marc; Loy, Alexander
Extensive richness and novel taxa of sulfoquinovose-degrading bacteria in the cow rumen Unpublished
bioRxiv, 2025.
@unpublished{Krasenbrink2025b,
title = {Extensive richness and novel taxa of sulfoquinovose-degrading bacteria in the cow rumen},
author = {Julia Krasenbrink and Song-Can Chen and Tomohisa Sebastian Tanabe and Huseyin Sarikece and Pleun Meurs and Sabrina Borusak and Rahul Samrat and Jay Osvatic and Joana Seneca and Bela Hausmann and Daan R Speth and Evelyne Selberherr and Wolfgang Wanek and David Schleheck and Marc Mussmann and Alexander Loy},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.05.20.655074},
doi = {10.1101/2025.05.20.655074},
year = {2025},
date = {2025-05-20},
urldate = {2025-05-20},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:p>Sulfoquinovose (SQ), a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol (SQDG), is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release SQ from SQDG. Despite its ecological importance, the diversity and functional roles of SQ-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments, including marine sediments and the mammalian gut. We revealed particularly high richness of yihQ-containing microorganisms in cow rumen, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of SQ metabolism in ruminant digestion. Anaerobic microcosm experiments with SQ-amended rumen fluid revealed cooperative microbial degradation of SQ to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics identified novel uncultured SQ-degrading taxa, including members of Caproiciproducens (Acutalibacteraceae), Limivicinus (Oscillospiraceae), and Sphaerochaetaceae, which encode the sulfo-transketolase pathway, along with Mailhella (Desulfovibrionaceae), a likely isethionate-respiring bacterium. This study presents the first functional gene-based assay for tracking environmental yihQ diversity, highlights SQ degradation as a central metabolic process in the cow rumen, describes novel SQ-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:p>Sulfoquinovose (SQ), a sulfonated sugar derived from the thylakoid membrane lipid sulfoquinovosyl diacylglycerol (SQDG), is abundant in photosynthetic organisms and plays a key role in global sulfur cycling. Its degradation in nature is mediated by specialized bacteria, many of which rely on the enzyme sulfoquinovosidase (YihQ) to release SQ from SQDG. Despite its ecological importance, the diversity and functional roles of SQ-degrading microorganisms remain poorly characterized in natural environments. Here, we developed a yihQ-targeted amplicon sequencing approach to investigate the richness and distribution of SQ-degrading bacteria across selected environments, including marine sediments and the mammalian gut. We revealed particularly high richness of yihQ-containing microorganisms in cow rumen, far exceeding that observed in human and mouse gut microbiomes, suggesting an important role of SQ metabolism in ruminant digestion. Anaerobic microcosm experiments with SQ-amended rumen fluid revealed cooperative microbial degradation of SQ to sulfide via isethionate cross-feeding. Amplicon sequencing and genome-resolved metagenomics identified novel uncultured SQ-degrading taxa, including members of Caproiciproducens (Acutalibacteraceae), Limivicinus (Oscillospiraceae), and Sphaerochaetaceae, which encode the sulfo-transketolase pathway, along with Mailhella (Desulfovibrionaceae), a likely isethionate-respiring bacterium. This study presents the first functional gene-based assay for tracking environmental yihQ diversity, highlights SQ degradation as a central metabolic process in the cow rumen, describes novel SQ-metabolizing bacteria, and advances understanding of sulfur physiology in complex microbial communities.</jats:p>
Ye, Huimin; Šlipogor, Vedrana; Hanson, Buck T.; Séneca, Joana; Hausmann, Bela; Herbold, Craig W.; Pjevac, Petra; Bugnyar, Thomas; Loy, Alexander
bioRxiv, 2025.
@unpublished{Ye2025,
title = {Associations between gut microbiota and personality traits: insights from a captive common marmoset (textitCallithrix jacchus) colony},
author = {Huimin Ye and Vedrana Šlipogor and Buck T. Hanson and Joana Séneca and Bela Hausmann and Craig W. Herbold and Petra Pjevac and Thomas Bugnyar and Alexander Loy},
url = {http://biorxiv.org/lookup/doi/10.1101/2025.02.12.637913},
doi = {10.1101/2025.02.12.637913},
year = {2025},
date = {2025-02-13},
urldate = {2025-02-13},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Abstract</jats:title><jats:p>Recent studies have suggested the link between inter-individual behavioural variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated links between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status and relatedness of 26 captive common marmosets (<jats:italic>Callithrix jacchus</jats:italic>), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genera<jats:italic>Desulfovibrio</jats:italic>were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene<jats:italic>dsrB</jats:italic>confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between selected microbial taxa and personality traits in captive common marmosets.</jats:p><jats:sec><jats:title>Importance</jats:title><jats:p>This study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential role of the gut microbiome in shaping or reflecting personality. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.</jats:p></jats:sec>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Abstract</jats:title><jats:p>Recent studies have suggested the link between inter-individual behavioural variation (i.e., animal personality) and gut microbiota. Non-human primates living under controlled conditions are valuable models to investigate diet-independent microbiome-host interactions. In this study, we investigated links between specific gut microbiota members and personality traits, as well as group membership, sex, age class, breeding status and relatedness of 26 captive common marmosets (<jats:italic>Callithrix jacchus</jats:italic>), maintained under the same diet and housing conditions. Personality was assessed using an established testing battery in repeated tests. Then, we collected a total of 225 fecal samples during the summers of 2017 and 2019 from five marmoset social groups for 16S rRNA gene amplicon sequencing. Within-individual microbiota variance was smaller than that between group members. Group members also exhibited more similar gut microbiota than individuals from different groups in each sampling year. Beta diversity of the gut microbiota was linked with personality traits, age class, sex, and breeding status, but not with genetic relatedness. We identified specific bacterial taxa associated with personality traits. In particular, members of the sulfite-reducing genera<jats:italic>Desulfovibrio</jats:italic>were enriched in more avoidant marmosets. Amplicon sequencing of the dissimilatory sulfite reductase gene<jats:italic>dsrB</jats:italic>confirmed this pattern, yet additionally revealed an unknown uncultured bacterium that was the predominant sulfite-reducing bacterium in the fecal samples and was linked to more explorative individuals. These findings highlight specific association patterns between selected microbial taxa and personality traits in captive common marmosets.</jats:p><jats:sec><jats:title>Importance</jats:title><jats:p>This study provides valuable insights into the intricate relationship between gut microbiota and host personality traits, using captive common marmosets as a model. By controlling for diet and housing conditions, it probes key host factors such as personality, age, sex, and social group membership, offering a robust framework for understanding microbiome-host interactions. The discovery of specific microbial taxa associated with personality traits, particularly the enrichment of sulfite-reducing genera in more avoidant individuals, underscores the potential role of the gut microbiome in shaping or reflecting personality. These findings advance our understanding of microbiome-host dynamics and pave the way for future research on the mechanistic links between behavior and gut microbiota in other animal models and across broader ecological contexts.</jats:p></jats:sec>
Jenab, Kian; Alteio, Lauren; Guseva, Ksenia; Gorka, Stefan; Darcy, Sean; Fuchslueger, Lucia; Canarini, Alberto; Martin, Victoria; Wiesenbauer, Julia; Spiegel, Felix; Imai, Bruna; Schmidt, Hannes; Hage-Ahmed, Karin; Pötsch, Erich M.; Richter, Andreas; Jansa, Jan; Kaiser, Christina
bioRxiv, 2024.
@unpublished{Jenab2024,
title = {Arbuscular mycorrhizal fungal families and exploration-based guilds exhibit distinct responses to N, P and K deficiencies and imbalances},
author = {Kian Jenab and Lauren Alteio and Ksenia Guseva and Stefan Gorka and Sean Darcy and Lucia Fuchslueger and Alberto Canarini and Victoria Martin and Julia Wiesenbauer and Felix Spiegel and Bruna Imai and Hannes Schmidt and Karin Hage-Ahmed and Erich M. Pötsch and Andreas Richter and Jan Jansa and Christina Kaiser},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.11.06.622229},
doi = {10.1101/2024.11.06.622229},
year = {2024},
date = {2024-11-08},
urldate = {2024-11-08},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:title>Summary</jats:title>
<jats:p> <jats:list list-type="bullet">
<jats:list-item>
<jats:p>Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after plant biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF), and the abundance of exploration-based AMF guilds (i.e., rhizophilic, edaphophilic, ancestral) remains largely unknown.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>We studied a 70-year nutrient-deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially, or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty-acid biomarkers, alongside soil and plant community properties.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing a 50% biomass reduction. We observed distinct guild- and family-specific responses: The edaphophilic guild declined with N deficiency, while the rhizophilic guild decreased with P and K deficiencies. Families within each guild, particularly in the ancestral guild, showed differential responses, indicating complementary nutrient specializations at the family level.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.</jats:p>
</jats:list-item>
</jats:list>
</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:title>Summary</jats:title>
<jats:p> <jats:list list-type=”bullet”>
<jats:list-item>
<jats:p>Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after plant biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF), and the abundance of exploration-based AMF guilds (i.e., rhizophilic, edaphophilic, ancestral) remains largely unknown.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>We studied a 70-year nutrient-deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially, or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty-acid biomarkers, alongside soil and plant community properties.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing a 50% biomass reduction. We observed distinct guild- and family-specific responses: The edaphophilic guild declined with N deficiency, while the rhizophilic guild decreased with P and K deficiencies. Families within each guild, particularly in the ancestral guild, showed differential responses, indicating complementary nutrient specializations at the family level.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.</jats:p>
</jats:list-item>
</jats:list>
</jats:p>
<jats:p> <jats:list list-type=”bullet”>
<jats:list-item>
<jats:p>Many agroecosystems face nitrogen (N), phosphorus (P) or potassium (K) deficiencies due to imbalanced or insufficient nutrient replenishment after plant biomass harvest. How this affects the symbiosis between plants and arbuscular mycorrhizal fungi (AMF), and the abundance of exploration-based AMF guilds (i.e., rhizophilic, edaphophilic, ancestral) remains largely unknown.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>We studied a 70-year nutrient-deficiency experiment in a managed grassland in central Austria, where aboveground biomass was harvested three times annually. N, P and K were fully, partially, or not replenished, causing long-term nutrient deficiencies and imbalances. We analysed AMF communities in soil and roots by DNA/RNA amplicon sequencing and fatty-acid biomarkers, alongside soil and plant community properties.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Soil AMF communities were affected by N and P deficiencies, while root AMF communities were most susceptible to K deficiency, showing a 50% biomass reduction. We observed distinct guild- and family-specific responses: The edaphophilic guild declined with N deficiency, while the rhizophilic guild decreased with P and K deficiencies. Families within each guild, particularly in the ancestral guild, showed differential responses, indicating complementary nutrient specializations at the family level.</jats:p>
</jats:list-item>
<jats:list-item>
<jats:p>Our findings underscore the previously unrecognized role of K deficiency in AMF symbiosis and suggest the existence of nutrient-related functional subgroups within exploration-based AMF guilds.</jats:p>
</jats:list-item>
</jats:list>
</jats:p>
Mahnert, Alexander; Dreer, Maximilian; Perier, Uelkue; Melcher, Michael; Duller, Stefanie; Lehnen, Adina; Goessler, Theodora; Brunner, Daniela; Graier, Thomas; Wolf, Peter; Ponce-Toledo, Rafael Isaac; Hodgskiss, Logan; Kerou, Melina; Moissl-Eichinger, Christine; Schleper, Christa
bioRxiv, 2024.
@unpublished{Mahnert2024b,
title = {Molecular Tracking and Cultivation Reveal Ammonia Oxidizing Archaea as Integral Members of the Human Skin Microbiome},
author = {Alexander Mahnert and Maximilian Dreer and Uelkue Perier and Michael Melcher and Stefanie Duller and Adina Lehnen and Theodora Goessler and Daniela Brunner and Thomas Graier and Peter Wolf and Rafael Isaac Ponce-Toledo and Logan Hodgskiss and Melina Kerou and Christine Moissl-Eichinger and Christa Schleper},
url = {http://biorxiv.org/lookup/doi/10.1101/2024.08.05.606590},
doi = {10.1101/2024.08.05.606590},
year = {2024},
date = {2024-08-05},
urldate = {2024-08-05},
publisher = {Cold Spring Harbor Laboratory},
abstract = {<jats:p>Ammonia oxidizing archaea (AOA) have been repeatedly detected in the human skin microbiome through molecular and biochemical analyses, yet their persistence, physiology, and adaptations remain poorly understood. Here, we describe two cultivated strains, Candidatus Nitrosocosmicus epidermidis and Ca. Nitrosocosmicus unguis, enriched from human skin samples. These autotrophic strains grow on ammonia and urea as sole energy sources. Genomic islands and expanded gene families in their genomes testify to the capacity of colonizing skin, including specific interactions with host proteins and signaling cascades that distinguish these AOA from their close relatives from soil. Molecular signatures of Nitrosocosmicus ssp. were consistently identified on individuals in cross-sectional and longitudinal cohorts (n=47) with a higher prevalence in sebaceous areas. Co-occurrence network patterns with specific bacteria reinforce the observation that AOA of the genus Nitrosocosmicus form a stable component of the healthy skin and represent emerging commensals in the human microbiome.</jats:p>},
howpublished = {bioRxiv},
keywords = {},
pubstate = {published},
tppubtype = {unpublished}
}
<jats:p>Ammonia oxidizing archaea (AOA) have been repeatedly detected in the human skin microbiome through molecular and biochemical analyses, yet their persistence, physiology, and adaptations remain poorly understood. Here, we describe two cultivated strains, Candidatus Nitrosocosmicus epidermidis and Ca. Nitrosocosmicus unguis, enriched from human skin samples. These autotrophic strains grow on ammonia and urea as sole energy sources. Genomic islands and expanded gene families in their genomes testify to the capacity of colonizing skin, including specific interactions with host proteins and signaling cascades that distinguish these AOA from their close relatives from soil. Molecular signatures of Nitrosocosmicus ssp. were consistently identified on individuals in cross-sectional and longitudinal cohorts (n=47) with a higher prevalence in sebaceous areas. Co-occurrence network patterns with specific bacteria reinforce the observation that AOA of the genus Nitrosocosmicus form a stable component of the healthy skin and represent emerging commensals in the human microbiome.</jats:p>
Kane, Alice E; Chellappa, Karthikeyani; Schultz, Michael B; Arnold, Matthew; Li, Jien; Amorim, Joao; Diener, Christian; Zhu, Dantong; Mitchell, Sarah J; Griffin, Patrick; Tian, Xiao; Petty, Christopher; Conway, Ryan; Walsh, Katie; Shelerud, Lukas; Duesing, Charlotte; Mueller, Amber; Li, Karlin; McNamara, Maeve; Shima, Rafaella T; Mitchell, James; Bonkowski, Michael S; Cabo, Rafael; Gibbons, Sean M; Wu, Lindsay E; Ikeno, Yuji; Baur, Joseph A; Rajman, Luis; Sinclair, David A
Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner Journal Article
In: bioRxiv, 2024, ISSN: 2692-8205.
@article{pmid38979132,
title = {Long-term NMN treatment increases lifespan and healthspan in mice in a sex dependent manner},
author = {Alice E Kane and Karthikeyani Chellappa and Michael B Schultz and Matthew Arnold and Jien Li and Joao Amorim and Christian Diener and Dantong Zhu and Sarah J Mitchell and Patrick Griffin and Xiao Tian and Christopher Petty and Ryan Conway and Katie Walsh and Lukas Shelerud and Charlotte Duesing and Amber Mueller and Karlin Li and Maeve McNamara and Rafaella T Shima and James Mitchell and Michael S Bonkowski and Rafael Cabo and Sean M Gibbons and Lindsay E Wu and Yuji Ikeno and Joseph A Baur and Luis Rajman and David A Sinclair},
doi = {10.1101/2024.06.21.599604},
issn = {2692-8205},
year = {2024},
date = {2024-06-01},
urldate = {2024-06-01},
journal = {bioRxiv},
abstract = {Nicotinamide adenine dinucleotide (NAD) is essential for many enzymatic reactions, including those involved in energy metabolism, DNA repair and the activity of sirtuins, a family of defensive deacylases. During aging, levels of NAD can decrease by up to 50% in some tissues, the repletion of which provides a range of health benefits in both mice and humans. Whether or not the NAD precursor nicotinamide mononucleotide (NMN) extends lifespan in mammals is not known. Here we investigate the effect of long-term administration of NMN on the health, cancer burden, frailty and lifespan of male and female mice. Without increasing tumor counts or severity in any tissue, NMN treatment of males and females increased activity, maintained more youthful gene expression patterns, and reduced overall frailty. Reduced frailty with NMN treatment was associated with increases in levels of a gut bacterium associated with lower inflammation in mice and increased longevity in humans. NMN slowed the accumulation of adipose tissue later in life and improved metabolic health in male but not female mice, while in females but not males, NMN increased median lifespan by 8.5%, possible due to sex-specific effects of NMN on NAD metabolism. Together, these data show that chronic NMN treatment delays frailty, alters the microbiome, improves male metabolic health, and increases female mouse lifespan, without increasing cancer burden. These results highlight the potential of NAD boosters for treating age-related conditions and the importance of using both sexes for interventional lifespan studies.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Nicotinamide adenine dinucleotide (NAD) is essential for many enzymatic reactions, including those involved in energy metabolism, DNA repair and the activity of sirtuins, a family of defensive deacylases. During aging, levels of NAD can decrease by up to 50% in some tissues, the repletion of which provides a range of health benefits in both mice and humans. Whether or not the NAD precursor nicotinamide mononucleotide (NMN) extends lifespan in mammals is not known. Here we investigate the effect of long-term administration of NMN on the health, cancer burden, frailty and lifespan of male and female mice. Without increasing tumor counts or severity in any tissue, NMN treatment of males and females increased activity, maintained more youthful gene expression patterns, and reduced overall frailty. Reduced frailty with NMN treatment was associated with increases in levels of a gut bacterium associated with lower inflammation in mice and increased longevity in humans. NMN slowed the accumulation of adipose tissue later in life and improved metabolic health in male but not female mice, while in females but not males, NMN increased median lifespan by 8.5%, possible due to sex-specific effects of NMN on NAD metabolism. Together, these data show that chronic NMN treatment delays frailty, alters the microbiome, improves male metabolic health, and increases female mouse lifespan, without increasing cancer burden. These results highlight the potential of NAD boosters for treating age-related conditions and the importance of using both sexes for interventional lifespan studies.
Carr, Alex; Baliga, Nitin S; Diener, Christian; Gibbons, Sean M
Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut Miscellaneous
2024, ISSN: 2692-8205.
@misc{pmid37162960,
title = {Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut},
author = {Alex Carr and Nitin S Baliga and Christian Diener and Sean M Gibbons},
doi = {10.1101/2023.04.28.538771},
issn = {2692-8205},
year = {2024},
date = {2024-01-01},
urldate = {2024-01-01},
journal = {bioRxiv},
abstract = {colonizes up to 30-40% of community-dwelling adults without causing disease. infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of colonization susceptibility or resistance and . MCMMs provide detailed mechanistic insights into the ecological interactions that govern engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 15,204 individuals from five independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to understand the mechanistic underpinnings of personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.},
keywords = {},
pubstate = {published},
tppubtype = {misc}
}
colonizes up to 30-40% of community-dwelling adults without causing disease. infections (CDIs) are the leading cause of antibiotic-associated diarrhea in the U.S. and typically develop in individuals following disruption of the gut microbiota due to antibiotic or chemotherapy treatments. Further treatment of CDI with antibiotics is not always effective and can lead to antibiotic resistance and recurrent infections (rCDI). The most effective treatment for rCDI is the reestablishment of an intact microbiota via fecal microbiota transplants (FMTs). However, the success of FMTs has been difficult to generalize because the microbial interactions that prevent engraftment and facilitate the successful clearance of are still only partially understood. Here we show how microbial community-scale metabolic models (MCMMs) accurately predicted known instances of colonization susceptibility or resistance and . MCMMs provide detailed mechanistic insights into the ecological interactions that govern engraftment, like cross-feeding or competition involving metabolites like succinate, trehalose, and ornithine, which differ from person to person. Indeed, three distinct metabolic niches emerge from our MCMMs, two associated with positive growth rates and one that represents non-growth, which are consistently observed across 15,204 individuals from five independent cohorts. Finally, we show how MCMMs can predict personalized engraftment and growth suppression for a probiotic cocktail (VE303) designed to replace FMTs for the treatment rCDI. Overall, this powerful modeling approach predicts personalized engraftment risk and can be leveraged to assess probiotic treatment efficacy. MCMMs could be extended to understand the mechanistic underpinnings of personalized engraftment of other opportunistic bacterial pathogens, beneficial probiotic organisms, or more complex microbial consortia.
Find us on social media
