Publications
2023
Araujo,
A. S. F., Jia, X., Miranda, A. R. L., Pereira, A. P.
D. A., Melo, V. M. M., Rocha, S. M. B., Costa, R. M., Saraiva, T.
C. D. S., Mendes, L. W., & Salles, J. F. (2023).
Changes in the bacterial rare biosphere after permanent
application of composted tannery sludge in a tropical soil.
Chemosphere, 313, Article 137487. https://doi.org/10.1016/j.chemosphere.2022.137487
Liu,
X., Hackl, T., & Salles, J. F.
(2023). Community coalescence altered the potential of
horizontal gene transfers within the native soil
microbiome. https://doi.org/10.1101/2023.09.18.558195
Mei,
S., Wang, M., Salles, J. F., & Hackl,
T. (2023). Diverse rhizosphere-associated
Pseudomonas genomes isolated along the marine-terrestrial
transition zone of a Wadden island salt march. BioRxiv.
https://doi.org/10.1101/2023.11.14.566819
Liu,
X., Mei, S., & Falcao Salles,
J. (2023). Inoculated microbial consortia perform
better than single strains in living soil: A meta-analysis.
Applied Soil Ecology, 190, Article
105011. https://doi.org/10.1016/j.apsoil.2023.105011
Li,
Y., Deng, X., Zhang, N., Shen, Z., Li, R., Shen, Q., &
Salles, J. F. (2023). Rhizosphere suppression hinders
antibiotic resistance gene (ARG) spread under bacterial
invasion. One Health, 16,
Article 100481. https://doi.org/10.1016/j.onehlt.2023.100481
van
der Goot, E. (2023). Phenylketonuria in a
microbial world: Gut-microbiome-brain interactions shaping behavior
in PKU. [Thesis fully internal (DIV), University of
Groningen]. University of Groningen. https://doi.org/10.33612/diss.678170132
Wang,
Y., Jiménez, D. J., Zhang, Z., &
van Elsas, J. D. (2023). Functioning of a tripartite
lignocellulolytic microbial consortium cultivated under two shaking
conditions: A metatranscriptomic study.
Biotechnology for Biofuels and Bioproducts,
16(1), Article 54. https://doi.org/10.1186/s13068-023-02289-0
2022
Gurung,
K., Vink, S. N., Salles, J.
F., & Wertheim, B. (2023). More
persistent bacterial than fungal associations in the microbiota of
a pest insect. Journal of Pest
Science, 96, 785–796. https://doi.org/10.1007/s10340-022-01524-1
Deng,
X., Zhang, N., Li, Y., Zhu, C., Qu, B., Liu, H., Li, R., Bai, Y.,
Shen, Q., & Falcao Salles, J. (2022).
Bio-organic soil amendment promotes the suppression of
Ralstonia solanacearum by inducing changes in the
functionality and composition of rhizosphere bacterial
communities. New Phytologist,
235(4), 1558-1574. https://doi.org/10.1111/nph.18221
Yu,
Y., van der Zwaag, M., Wedman, J.
J., Permentier, H., Plomp,
N., Jia, X., Kanon, B.,
Eggens-Meijer, E., Buist, G., Harmsen,
H., Kok, J., Salles, J. F.,
Wertheim, B., Hayflick, S. J., Strauss,
E., Grzeschik, N. A., Schepers, H.,
& Sibon, O. C. M. (2022). Coenzyme A precursors
flow from mother to zygote and from microbiome to host.
Molecular Cell, 82(14),
2650-2665.e12. https://doi.org/10.1016/j.molcel.2022.05.006
Saatkamp,
H. W., Aartsma, Y., Hogeveen, H., Augustijn, M., Baumann, A.,
Beukeboom, L. W., Borghuis, A., Bovenkerk, B., van der
Bruggen, M., Companjen, M. H., Dörper, A.,
Salles, J. F., van der Fels-Klerx, H. J., Fischer, A. R. H.,
Haenen, O., Hosseini, A., van den Hurk, J., Jacobs, P., Jansen, W.
L., ... Dicke, M. (2022). Development of sustainable business
models for insect-fed poultry production: opportunities and
risks. Journal of Insects as Food and
Feed, 8(12), 1469-1483. https://doi.org/10.3920/JIFF2021.0216
van
der Goot, E., Vink, S. N., van Vliet, D.,
van Spronsen, F. J., Falcao Salles, J.,
& van der Zee, E. A. (2022). Gut-microbiome
composition in response to phenylketonuria depends on dietary
phenylalanine in BTBR Pahenu2 mice.
Frontiers in nutrition, 8, Article
735366. https://doi.org/10.3389/fnut.2021.735366
Dietz,
M., Matson, K., Versteegh, M., van der
Velde, M., Parmentier, H. K., Arts, J. A. J., Falcao
Salles, J., & Tieleman, I. (2022).
Gut microbiota of homing pigeons shows summer-winter
variation under constant diet indicating a substantial effect of
temperature. (bioRxiv). BioRxiv. https://doi.org/10.1101/2022.05.18.492417
Dietz,
M., Matson, K. D., Versteegh, M., van der
Velde, M., Parmentier, H. K., Arts, J. A. J., Falcao
Salles, J., & Tieleman, B. I. (2022).
Gut microbiota of homing pigeons shows summer–winter
variation under constant diet indicating a substantial effect of
temperature. Animal microbiome,
4, Article 64. https://doi.org/10.1186/s42523-022-00216-6
Vogel,
M., Shah, P. N., Voulgari-Kokota, A., Maistrou,
S., Aartsma, Y., Beukeboom, L. W., Salles, J.
F., van Loon, J. J. A., Dicke, M., & Wertheim,
B. (2022). Health of the black soldier fly and house
fly under mass-rearing conditions: Innate immunity and the role of
the microbiome. Journal of Insects as Food and
Feed, 8(8), 857-878. https://doi.org/10.3920/JIFF2021.0151
Voulgari-Kokota,
A., Beukeboom, L. W., Wertheim,
B., & Salles, J. F. (2022).
Houseflies harbor less diverse microbiota under laboratory
conditions but maintain a consistent set of host-associated
bacteria. Scientific Reports,
12(1), Article 11132. https://doi.org/10.1038/s41598-022-15186-7
Mawarda,
P. C., Mallon, C. A., Le Roux, X., van
Elsas, J. D., & Salles, J. F. (2022).
Interactions between bacterial inoculants and native soil
bacterial community: The case of spore-forming Bacillus
spp. FEMS microbiology ecology,
98(12), 1-11. https://doi.org/10.1093/femsec/fiac127
Brinker,
P., Chen, F., Ben Chehida, Y., Beukeboom,
L., Fontaine, M., & Falcao Salles,
J. (2022). Microbiome composition is shaped by
geography and population structure in the parasitic wasp Asobara
japonica , but not in the presence of the endosymbiont
Wolbachia. Molecular Ecology.
Advance online publication. https://doi.org/10.1111/mec.16699
Bisschop,
K., Kortenbosch, H. H., van Eldijk, T. J.
B., Mallon, C. A., Salles, J. F.,
Bonte, D., & Etienne, R. S. (2022).
Microbiome heritability and its role in adaptation of hosts
to novel resources. Frontiers in
Microbiology, 13, 703183. Article 703183. https://doi.org/10.3389/fmicb.2022.703183
Frąc,
M., Hannula, E. S., Bełka, M., Salles, J. F.,
& Jedryczka, M. (2022). Soil mycobiome in sustainable
agriculture. Frontiers in
Microbiology, 13, Article 1033824. https://doi.org/10.3389/fmicb.2022.1033824
Mawarda,
P., Lakke, S. L., van Elsas, J. D., &
Falcao Salles, J. (2022). Temporal dynamics of the
soil bacterial community following Bacillus invasion.
iScience , 25(5), Article 104185. https://doi.org/10.1016/j.isci.2022.104185
Mawarda,
P. C., Le Roux, X., Uribe Acosta, M., van Elsas, J.
D., & Falcao Salles, J. (2022). The
impact of protozoa addition on the survivability of Bacillus
inoculants and soil microbiome dynamics. ISME
Communications, 2, Article 82 (2022). https://doi.org/10.1038/s43705-022-00166-9
Liu,
X., Le Roux, X., & Salles, J. F. (2022).
The legacy of microbial inoculants in agroecosystems and
potential for tackling climate change challenges.
Iscience, 25(3), Article 103821. https://doi.org/10.1016/j.isci.2022.103821
van
Veelen, H. P. J., Salles, J. F., Matson, K.
D., van Doorn, G. S., van der Velde,
M., & Tieleman, B. I. (2022). The
microbial environment modulates non-genetic maternal effects on egg
immunity. Animal microbiome,
4(1), Article 44. https://doi.org/10.1186/s42523-022-00195-8
Jia,
X., Dini-Andreote, F., & Salles, J. F.
(2022). Unravelling the interplay of ecological processes
structuring the bacterial rare biosphere. ISME
Communications, 2(1), Article 96. https://doi.org/10.1038/s43705-022-00177-6
Brinker,
P. (2022). Complex interactions in a
host-symbiont-microbiome triangle: The wasp Asobara
japonica, the endosymbiont Wolbachia and the remainder
microbiome. [Thesis fully internal (DIV), University of
Groningen]. University of Groningen. https://doi.org/10.33612/diss.240460364
Chen,
Q. (2022). Arbuscular mycorrhizal fungus
Rhizophagus irregularis and soil bacteriome interactions
affecting maize (Zea mays L.) under saline
conditions. [Thesis fully internal (DIV), University of
Groningen]. University of Groningen. https://doi.org/10.33612/diss.195172017
Chen,
Q., Deng, X., Elzenga, J. T. M., &
van Elsas, J. D. (2022). Effect of soil bacteriomes on
mycorrhizal colonization by Rhizophagus irregularis:
Interactive effects on maize (Zea mays L.) growth under salt
stress. Biology and Fertility of Soils
, 58, 515-525. https://doi.org/10.1007/s00374-022-01636-x
Garcia-Hernandez,
D. E. (2022). Dynamics of salt marsh biomes in
response to inundation. [Thesis fully internal (DIV),
University of Groningen]. University of Groningen. https://doi.org/10.33612/diss.195824597
Angulo,
V., Beriot, N., Garcia-Hernandez, E., Li, E.,
Masteling, R., & Lau, J. A. (2022). Plant-microbe
eco-evolutionary dynamics in a changing world. New
Phytologist, 234(6), 1919-1928. https://doi.org/10.1111/nph.18015
Gurung,
K. (2022). A microbial perspective of
Drosophila suzukii: Insights into the pest microbe
interactions. [Thesis fully internal (DIV), University
of Groningen]. University of Groningen. https://doi.org/10.33612/diss.240675623
Mawarda,
P. C. (2022). The soil microbiome dynamics
following microbial invasions. [Thesis fully internal
(DIV), University of Groningen]. University of Groningen. https://doi.org/10.33612/diss.240051264
Wang,
Y. (2022). Functioning of a synthetic
lignocellulolytic microbial consortium: The effect of conditions on
dynamics of interactions and functioning. [Thesis fully
internal (DIV), University of Groningen]. University of Groningen.
https://doi.org/10.33612/diss.231637581
2021
Oberman,
K., Hovens, I., de Haan, J.,
Falcao-Salles, J., van Leeuwen, B., &
Schoemaker, R. (2021). Acute pre-operative ibuprofen
improves cognition in a rat model for postoperative cognitive
dysfunction. Journal of
neuroinflammation, 18(1), 1-13. Article 156.
https://doi.org/10.1186/s12974-021-02206-y
Vink,
S. N., Chrysargyris, A., Tzortzakis, N., & Salles,
J. F. (2021). Bacterial community dynamics varies with
soil management and irrigation practices in grapevines (Vitis
vinifera L.). Applied Soil
Ecology, 158, Article 103807. https://doi.org/10.1016/j.apsoil.2020.103807
Hovens,
I. B., van Leeuwen, B. L., Falcao-Salles,
J., de Haan, J. J., & Schoemaker, R.
G. (2021). Enteral enriched nutrition to prevent
cognitive dysfunction after surgery: A study in rats.
Brain, behavior, & immunity - health,
16, Article 100305. https://doi.org/10.1016/j.bbih.2021.100305
Vink,
S. N., Dini-Andreote, F., Höfle, R., Kicherer,
A., & Salles, J. F. (2021). Interactive
effects of scion and rootstock genotypes on the root microbiome of
grapevines (Vitis spp. L.). Applied
Sciences, 11(4), Article 1615. https://doi.org/10.3390/app11041615
García
Hernández, E., Berg, M. P., Van Oosten, A.
R., Smit, C., & Falcão Salles,
J. (2021). Linking bacterial communities associated
with the environment and the ecosystem engineer Orchestia
gammarellus at contrasting salt marsh elevations.
Microbial ecology, 82, 537-548. https://doi.org/10.1007/s00248-020-01656-w
Hendriks,
K. P., Bisschop, K., Kavanagh, J. C.,
Kortenbosch, H. H., Larue, A. E. A., Bonte, D., Duijm, E.
J., Salles, J. F., Richter Mendoza, F.
J., Schilthuizen, M., & Etienne, R. S.
(2021). Plant diets of land snail community members are
similar in composition but differ in richness.
Journal of Molluscan Studies, 87(4),
Article eyab041. https://doi.org/10.1093/mollus/eyab041
Deng,
X., Zhang, N., Shen, Z., Zhu, C., Liu, H., Xu, Z., Li, R., Shen,
Q., & Salles, J. F. (2021). Soil microbiome
manipulation triggers direct and possible indirect suppression
against Ralstonia solanacearum and Fusarium
oxysporum. NPJ biofilms and
microbiomes, 7(1), Article 33. https://doi.org/10.1038/s41522-021-00204-9
Wang,
Y., Brons, J. K., & van Elsas, J.
D. (2021). Considerations on the identity and
diversity of organisms affiliated with Sphingobacterium
multivorum: Proposal for a new species, Sphingobacterium
paramultivorum. Microorganisms,
9(10), Article 2057. https://doi.org/10.3390/microorganisms9102057
Zandbergen,
L., Brons, J., Halverson, T., Wolfe, A.
J., & de Vos, M. (2021). The good and the
bad: Ecological interaction measurements between the urinary
microbiota and uropathogens. Frontiers in
Microbiology, 12, Article 659450. https://doi.org/10.3389/fmicb.2021.659450
van
Vliet, D., van der Goot, E., van Ginkel, W.
G., van Faassen, H. J. R., de Blaauw, P.,
Kema, I. P., Heiner-Fokkema, M. R., van
der Zee, E. A., & van Spronsen, F. J.
(2022). The increasing importance of LNAA supplementation in
phenylketonuria at higher plasma phenylalanine
concentrations. Molecular Genetics and
Metabolism, 135(1), 27-34. https://doi.org/10.1016/j.ymgme.2021.11.003
Dijkstra,
A. M., van Vliet, N., van Vliet, D., Romani, C., Huijbregts,
S. C. J., van der Goot, E., Hovens, I.
B., van der Zee, E. A., Kema, I.
P., Heiner-Fokkema, M. R., & van
Spronsen, F. J. (2021). Correlations of blood and
brain biochemistry in phenylketonuria: Results from the Pah-enu2
PKU mouse. Molecular Genetics and
Metabolism, 134(3), 250-256. https://doi.org/10.1016/j.ymgme.2021.09.004
Jia,
X. (2021). Soil bacterial community assembly
during succession. [Thesis fully internal (DIV),
University of Groningen]. University of Groningen. https://doi.org/10.33612/diss.156586683
Wang,
Y., Elzenga, T., & van Elsas, J.
D. (2021). Effect of culture conditions on the
performance of lignocellulose-degrading synthetic microbial
consortia. Applied Microbiology and
Biotechnology, 105, 7981–7995. https://doi.org/10.1007/s00253-021-11591-6
2020
Hendriks,
K. P., Bisschop, K., Kortenbosch, H.
H., Kavanagh, J. C., Larue, A. E. A., Phung, C-C., Bonte,
D., Duijm, E. J., Falcão Salles, J., Pigot, A.
L., Richter Mendoza, F. J., Schilthuizen, M.,
Anderson, M. J., Speksnijder, A. G. C. L., & Etienne, R.
S. (2021). Microbiome and environment explain the
absence of correlations between consumers and their diet in Bornean
microsnails. Ecology, 102(2),
Article e03237. https://doi.org/10.1002/ecy.3237
Ferreira,
D. A., da Silva, T. F., Pylro, V. S., Salles, J. F.,
Andreote, F. D., & Dini-Andreote, F. (2021). Soil
microbial diversity affects the plant-root colonization by
arbuscular mycorrhizal fungi. Microbial
ecology, 82, 100–103. https://doi.org/10.1007/s00248-020-01502-z
Xing,
J., Jia, X., Wang, H., Ma, B., Salles, J.
F., & Xu, J. (2021). The legacy of bacterial
invasions on soil native communities.
Environmental Microbiology, 23(2),
669-681. https://doi.org/10.1111/1462-2920.15086
Jurburg,
S. D., Assemien, F. L., Beaumelle, L., Salles, J.
F., van Elsas, J. D., & Le Roux, X. (2020).
A history of extreme disturbance affects the relationship
between the abundances of nitrifiers in soil.
Biology and Fertility of Soils ,
56(8), 1177-1187. https://doi.org/10.1007/s00374-020-01491-8
van
der Goot, E., van Spronsen, F. J.,
Falcão Salles, J., & van der Zee, E.
A. (2020). A microbial community ecology perspective
on the gut-microbiome-brain axis. Frontiers in
endocrinology, 11, 611. Article 611. https://doi.org/10.3389/fendo.2020.00611
Cortes-Tolalpa,
L., Wang, Y., Salles, J. F., &
van Elsas, J. D. (2020). Comparative genome analysis
of the lignocellulose degrading bacteria Citrobacter
freundii so4 and Sphingobacterium multivorum w15.
Frontiers in Microbiology, 11, 248.
Article 248. https://doi.org/10.3389/fmicb.2020.00248
Jia,
X., Dini-Andreote, F., & Falcão Salles,
J. (2020). Comparing the influence of assembly
processes governing bacterial community succession based on DNA and
RNA data. Microorganisms,
8(6), Article 798. https://doi.org/10.3390/microorganisms8060798
Mawarda,
P. C., Le Roux, X., van Elsas, J. D.,
& Salles, J. F. (2020). Deliberate introduction of
invisible invaders: A critical appraisal of the impact of microbial
inoculants on soil microbial communities. Soil
Biology and Biochemistry, 148, Article 107874.
https://doi.org/10.1016/j.soilbio.2020.107874
Engel,
F. G., Dini-Andreote, F., Eriksson, B. K.,
Salles, J. F., de Lima Brossi, M. J., & Matthiessen, B.
(2020). Dispersal mitigates bacterial dominance over
microalgal competitor in metacommunities.
Oecologia, 193(3), 677-687. https://doi.org/10.1007/s00442-020-04707-8
Dicke,
M., Eilenberg, J., Salles, J. F., Jensen, A. B.,
Lecocq, A., Pijlman, G. P., van Loon, J. J. A., & van Oers, M.
M. (2020). Edible insects unlikely to contribute to
transmission of coronavirus SARS-CoV-2. Journal of
Insects as Food and Feed, 6(4), 333-339. https://doi.org/10.3920/JIFF2020.0039
van
Veelen, H. P. J., Falcão Salles, J.,
Matson, K. D., van der Velde, M., &
Tieleman, B. I. (2020). Microbial environment shapes
immune function and cloacal microbiota dynamics in zebra finches
Taeniopygia guttata. Animal
microbiome, 2(1), Article 21. https://doi.org/10.1186/s42523-020-00039-3
Deng,
X., Zhang, N., Shen, Z., Zhu, C., Li, R., Salles, J.
F., & Shen, Q. (2020). Rhizosphere bacteria
assembly derived from fumigation and organic amendment triggers the
direct and indirect suppression of tomato bacterial wilt
disease. Applied Soil Ecology,
147, Article 103364. https://doi.org/10.1016/j.apsoil.2019.103364
Hernández,
E. G., Baraza, E., Smit, C., Berg, M.
P., & Falcão Salles, J. (2020).
Salt marsh elevation drives root microbial composition of the
native invasive grass Elytrigia atherica.
Microorganisms, 8(10), 1-19. Article
1619. https://doi.org/10.3390/microorganisms8101619
Pratama,
A. A., Terpstra, J., de Oliveria, A. L. M., & Salles, J.
F. (2020). The role of rhizosphere bacteriophages in
plant health. Trends in Microbiology,
28(9), 709-718. https://doi.org/10.1016/j.tim.2020.04.005
Sternhagen,
E. C., Black, K. L., Hartmann , E. DL., Shivega, W. G., Johnson, P.
G., McGlynn, R. D., Schmaltz, L. C., Asheim Keller, R. J.,
Vink, S. N., & Aldrich-Wolfe, L. (2020).
Contrasting patterns of functional diversity in coffee root
fungal communities associated with organic and conventionally
managed fields. Applied and environmental
microbiology, 86(11), Article 5220. https://doi.org/10.1128/AEM.00052-20
Brons,
J., Vink, S. N., de Vos, M.,
Reuter, S., Dobrindt, U., & van Elsas, J. D.
(2020). Fast identification of Escherichia coli in
urinary tract infections using a virulence gene based PCR approach
in a novel thermal cycler. Journal of
microbiological methods, 169, Article 105799.
https://doi.org/10.1016/j.mimet.2019.105799
Vink,
S. N., Bienkowski, D., Roberts, D. M., Daniell, T. J., &
Neilson, R. (2020). Impact of land use and management
practices on soil nematode communities of Machair, a low-input
calcareous ecosystem of conservation importance.
Science of the Total Environment,
738, Article 140164. https://doi.org/10.1016/j.scitotenv.2020.140164
Aldrich-Wolfe,
L., Black, K. L., Hartmann, E. D. L., Shivega, W. G., Schmaltz, L.
C., McGlynn, R. D., Johnson, P. G., Asheim Keller, R. J.,
& Vink, S. N. (2020). Taxonomic shifts in
arbuscular mycorrhizal fungal communities with shade and soil
nitrogen across conventionally managed and organic coffee
agroecosystems. Mycorrhiza,
30(4), 513-527. https://doi.org/10.1007/s00572-020-00967-7
Tragust,
S., Brinker, P., Rossel, N., & Otti, O. (2020).
Balancing life history investment decisions in founding ant
queens. Frontiers in Ecology and
Evolution, 8, Article 76. https://doi.org/10.3389/fevo.2020.00076
Pratama,
A. A., Javier Jimenez, D., Chen, Q., Bunk, B.,
Sproeer, C., Overmann, J., & van Elsas, J. D.
(2020). Delineation of a subgroup of the genus
Paraburkholderia, including P. terrae DSM 17804(T),
P. hospita DSM 17164(T), and four soil-isolated fungiphiles,
reveals remarkable genomic and ecological features: Proposal for
the definition of a P. hospita species cluster.
Genome Biology and Evolution, 12(4),
325-344. https://doi.org/10.1093/gbe/evaa031
Jimenez,
D. J., Wang, Y., Chaib de Mares, M., Cortes-Tolalpa,
L., Mertens, J. A., Hector, R. E., Lin, J., Johnson, J., Lipzen,
A., Barry, K., Mondo, S. J., Grigoriev, I., Nichols, N. N.,
& van Elsas, J. D. (2020). Defining the
eco-enzymological role of the fungal strain Coniochaeta sp.
2T2.1 in a tripartite lignocellulolytic microbial
consortium. FEMS microbiology ecology,
96(1), Article 186. https://doi.org/10.1093/femsec/fiz186
2019
Puentes-Tellez,
P. E., & Salles, J. F. (2020). Dynamics of
abundant and rare bacteria during degradation of lignocellulose
from sugarcane biomass. Microbial
ecology, 79(2), 312-325. https://doi.org/10.1007/s00248-019-01403-w
Dietz,
M. W., Salles, J. F., Hsu, B-Y., Dijkstra,
C., Groothuis, T. G. G., van der Velde,
M., Verkuil, Y. I., & Tieleman, B.
I. (2020). Prenatal transfer of gut bacteria in Rock
pigeon. Microorganisms, 8(1),
Article 61. https://doi.org/10.3390/microorganisms8010061
Kyselkova,
M., Salles, J. F., Dumestre, A., Benoit, Y., &
Grundmann, G. L. (2019). Distinct bacterial consortia
established in ETBE-degrading enrichments from a polluted
aquifer. Applied Sciences,
9(20). https://doi.org/10.3390/app9204247
Brinker,
P., Fontaine, M. C., Beukeboom, L.
W., & Salles, J. F. (2019). Host,
symbionts, and the microbiome: The missing tripartite
interaction. Trends in Microbiology,
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