Staff Publications

Staff Publications

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    'Staff publications' is the digital repository of Wageningen University & Research

    'Staff publications' contains references to publications authored by Wageningen University staff from 1976 onward.

    Publications authored by the staff of the Research Institutes are available from 1995 onwards.

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    We will mail you new results for this query: keywords==16S rRNA
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Archaeal and bacterial diversity and community composition from 18 phylogenetically divergent sponge species in Vietnam
Dat, Ton That Huu ; Steinert, Georg ; Cuc, Nguyen Thi Kim ; Smidt, Hauke ; Sipkema, Detmer - \ 2018
PeerJ 6 (2018). - ISSN 2167-8359
16S rRNA - Porifera - Prokaryotic diversity - Symbiosis - Vietnam
Sponge-associated prokaryotic diversity has been studied from a wide range of marine environments across the globe. However, for certain regions, e.g., Vietnam, Thailand, Cambodia, and Singapore, an overview of the sponge-associated prokaryotic communities is still pending. In this study we characterized the prokaryotic communities from 27 specimens, comprising 18 marine sponge species, sampled from the central coastal region of Vietnam. Illumina MiSeq sequencing of 16S ribosomal RNA (rRNA) gene fragments was used to investigate spongeassociated bacterial and archaeal diversity. Overall, 14 bacterial phyla and one archaeal phylum were identified among all 27 samples. The phylum Proteobacteria was present in all sponges and the most prevalent phylum in 15 out of 18 sponge species, albeit with pronounced differences at the class level. In contrast, Chloroflexi was the most abundant phylum in Halichondria sp., whereas Spirastrella sp. and Dactylospongia sp. were dominated by Actinobacteria. Several bacterial phyla such as Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Deferribacteres, Gemmatimonadetes, and Nitrospirae were found in two-thirds of the sponge species. Moreover, the phylum Thaumarchaeota (Archaea), which is known to comprise nitrifying archaea, was highly abundant among the majority of the 18 investigated sponge species. Altogether, this study demonstrates that the diversity of prokaryotic communities associated with Vietnamese sponges is comparable to spongeprokaryotic assemblages from well-documented regions. Furthermore, the phylogenetically divergent sponges hosted species-specific prokaryotic communities, thus demonstrating the influence of host identity on the composition and diversity of the associated communities. Therefore, this high-throughput 16S rRNA gene amplicon analysis of Vietnamese sponge-prokaryotic communities provides a foundation for future studies on sponge symbiont function and sponge-derived bioactive compounds from this region.
Host and environmental factors affecting the intestinal microbiota in chickens
Kers, Jannigje G. ; Velkers, Francisca C. ; Fischer, Egil A.J. ; Hermes, Gerben D.A. ; Stegeman, J.A. ; Smidt, Hauke - \ 2018
Frontiers in Microbiology 9 (2018)FEB. - ISSN 1664-302X
16S rRNA - Confounding factors - Gut health - Gut microbiota - Microbiome - Poultry
The initial development of intestinal microbiota in poultry plays an important role in production performance, overall health and resistance against microbial infections. Multiplexed sequencing of 16S ribosomal RNA gene amplicons is often used in studies, such as feed intervention or antimicrobial drug trials, to determine corresponding effects on the composition of intestinal microbiota. However, considerable variation of intestinal microbiota composition has been observed both within and across studies. Such variation may in part be attributed to technical factors, such as sampling procedures, sample storage, DNA extraction, the choice of PCR primers and corresponding region to be sequenced, and the sequencing platforms used. Furthermore, part of this variation in microbiota composition may also be explained by different host characteristics and environmental factors. To facilitate the improvement of design, reproducibility and interpretation of poultry microbiota studies, we have reviewed the literature on confounding factors influencing the observed intestinal microbiota in chickens. First, it has been identified that host-related factors, such as age, sex, and breed, have a large effect on intestinal microbiota. The diversity of chicken intestinal microbiota tends to increase most during the first weeks of life, and corresponding colonization patterns seem to differ between layer- and meat-type chickens. Second, it has been found that environmental factors, such as biosecurity level, housing, litter, feed access and climate also have an effect on the composition of the intestinal microbiota. As microbiota studies have to deal with many of these unknown or hidden host and environmental variables, the choice of study designs can have a great impact on study outcomes and interpretation of the data. Providing details on a broad range of host and environmental factors in articles and sequence data repositories is highly recommended. This creates opportunities to combine data from different studies for meta-analysis, which will facilitate scientific breakthroughs toward nutritional and husbandry associated strategies to improve animal health and performance.
Responses of soil bacterial community after seventh yearly applications of composted tannery sludge
Miranda, Ana Roberta Lima ; Mendes, Lucas William ; Rocha, Sandra Mara Barbosa ; Brink, Paul J. Van den; Bezerra, Walderly Melgaço ; Melo, Vania Maria Maciel ; Antunes, Jadson Emanuel Lopes ; Araujo, Ademir Sergio Ferreira - \ 2018
Geoderma 318 (2018). - ISSN 0016-7061 - p. 1 - 8.
16S rRNA - Organic waste - Soil microbial diversity
Composted tannery sludge (CTS) contains organic compounds and inorganic elements, mainly chromium (Cr), and its long-term application in soil can alter the bacterial structure and diversity. Thus, we used the next-generation sequencing to assess the structure and diversity of bacterial communities in soils after 7 years of CTS application. CTS was applied at 0, 2.5, 5, 10, and 20 Mg ha− 1 and the soil samples were collected at 75 days after application in the seventh year. The most abundant phyla were Actinobacteria, Proteobacteria, Firmicutes, and Chloroflexi. The abundance of some specific groups increased with application of CTS, such as Anaerolinea S0208 and Firmicutes. Six bacterial genera differed between amended and unamended soil. The abundance of Bacillus, Paenibacillus, Symbiobacterium, Clostridium, Microlunatus, and Actinomadura increased after application of CTS. The Redundancy Analysis between the structure of the bacterial community and chemical variables in soil did not cluster all treatments clearly, but showed Cr, pH, and organic C as significant chemical variables that influenced the bacterial communities. Application of CTS in soil has a primary effect on the bacterial communities that, negatively, alter the bacterial diversity and community similarity, while that, positively, it permits to select specific bacterial groups able to resist and biodegrade contaminants.
Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils
Schlemper, Thiago R. ; Leite, Márcio F.A. ; Lucheta, Adriano R. ; Shimels, Mahdere ; Bouwmeester, Harro J. ; Veen, Johannes A. van; Kuramae, Eiko E. - \ 2017
FEMS Microbiology Ecology 93 (2017)8. - ISSN 0168-6496
16S rRNA - bacterial community composition - next-generation sequencing - Sorghum genotypes; rhizosphere - strigolactone
Plant genotype selects the rhizosphere microbiome. The success of plant-microbe interactions is dependent on factors that directly or indirectly influence the plant rhizosphere microbial composition. We investigated the rhizosphere bacterial community composition of seven different sorghum cultivars in two different soil types (abandoned (CF) and agricultural (VD)). The rhizosphere bacterial community was evaluated at four different plant growth stages: emergence of the second (day 10) and third leaves (day 20), the transition between the vegetative and reproductive stages (day 35), and the emergence of the last visible leaf (day 50). At early stages (days 10 and 20), the sorghum rhizosphere bacterial community composition was mainly driven by soil type, whereas at late stages (days 35 and 50), the bacterial community composition was also affected by the sorghum genotype. Although this effect of sorghum genotype was small, different sorghum cultivars assembled significantly different bacterial community compositions. In CF soil, the striga-resistant cultivar had significantly higher relative abundances of Acidobacteria GP1, Burkholderia, Cupriavidus (Burkholderiaceae), Acidovorax and Albidiferax (Comamonadaceae) than the other six cultivars. This study is the first to simultaneously investigate the contributions of plant genotype, plant growth stage and soil type in shaping sorghum rhizosphere bacterial community composition.
Ratio of Klebsiella/Bifidobacterium in early life correlates with later development of paediatric allergy
Low, J.S.Y. ; Soh, S.E. ; Lee, Y.K. ; Kwek, K.Y.C. ; Holbrook, J.D. ; Beek, E.M. Van der; Shek, L.P. ; Goh, A.E.N. ; Teoh, O.H. ; Godfrey, K.M. ; Chong, Y.S. ; Knol, J. ; Lay, C. - \ 2017
Beneficial Microbes 8 (2017)5. - ISSN 1876-2883 - p. 681 - 695.
16S rRNA - Atopic dermatitis - Bifidobacterium spp - Eczema - Enterobacteriaceae
Several studies have reported that intestinal microbial colonisation patterns differ between non-allergic and allergic infants. However, the microbial signature underlying the pathogenesis of allergies remains unclear. We aim to gain insight into the development of the intestinal microbiota of healthy infants and infants who develop allergy in early life, and identify potential microbiota biomarkers of later allergic disease. Using a case-control design in a Chinese sub-cohort of a Singaporean birth cohort (GUSTO), we utilised 16S rRNA gene sequencing to assess intestinal microbial composition and diversity of 21 allergic and 18 healthy infants at 3 weeks, 3 months and 6 months of age, and correlated the microbiota with allergy at ages 18 and 36 months. Pronounced differences in intestinal microbiota composition between allergic and healthy infants were observed at 3 months of age. The intestine of healthy infants was colonised with higher abundance of commensal Bifidobacterium. Conversely, Klebsiella, an opportunistic pathogen, was significantly enriched in the allergic infants. Interestingly, infants with a high Klebsiella/Bifidobacterium (K/B) ratio (above the population median K/B ratio) at age 3 months had an odds ratio of developing allergy by 3 years of age of 9.00 (95% confidence interval 1.46-55.50) compared to those with low K/B ratio. This study demonstrated a relationship between the ratio of genera Klebsiella and Bifidobacterium during early infancy and development of paediatric allergy in childhood. Our study postulates that an elevated K/B ratio in early infancy could be a potential indicator of an increased risk of allergy development. This line of research might enable future intervention strategies in early life to prevent or treat allergy. Our study provides new insights into microbial signatures associated with childhood allergy, in particular, suggests that an elevated K/B ratio could be a potential early-life microbiota biomarker of allergic disease.
BLAST results most abundant 97% OTUs
Steinert, G. ; Taylor, Michael W. ; Deines, Peter ; Simister, Rachel L. ; Voogd, Nicole J. De; Hoggard, Michael ; Schupp, Peter J. - \ 2017
16S rRNA - NCBI blast - greengenes
Top 30 OTUs, sequences & best BLAST hits (nr/nt)
Guam Sponge Microbial OTU abundance & Taxonomy (Greengenes)
Steinert, G. ; Taylor, Michael W. ; Deines, Peter ; Simister, Rachel L. ; Voogd, Nicole J. De; Hoggard, Michael ; Schupp, Peter J. - \ 2016
OTU table - 16S rRNA - greengenes - taxonomy - sponges
16S rRNA gene OTU (97%) Greengenes classification and abundance table of sponge associated microbial communities from Guam (USA) - 2247 OTUs
In four shallow and mesophotic tropical reef sponges from Guam the microbial community largely depends on host identity
Steinert, Georg ; Taylor, Michael W. ; Deines, Peter ; Simister, Rachel L. ; Voogd, Nicole J. De; Hoggard, Michael ; Schupp, Peter J. - \ 2016
PeerJ 2016 (2016)4. - ISSN 2167-8359
16S rRNA - Environmental variability - Microbial diversity - Porifera - Pyrosequencing - Symbiosis

Sponges (phylum Porifera) are important members of almost all aquatic ecosystems, and are renowned for hosting often dense and diverse microbial communities. While the specificity of the sponge microbiota seems to be closely related to host phylogeny, the environmental factors that could shape differences within local sponge-specific communities remain less understood. On tropical coral reefs, sponge habitats can span from shallow areas to deeper, mesophotic sites. These habitats differ in terms of environmental factors such as light, temperature, and food availability, as well as anthropogenic impact. In order to study the host specificity and potential influence of varying habitats on the sponge microbiota within a local area, four tropical reef sponges, Rhabdastrella globostellata, Callyspongia sp., Rhaphoxya sp., and Acanthella cavernosa, were collected from exposed shallow reef slopes and a deep reef drop-off. Based on 16S rRNA gene pyrosequencing profiles, beta diversity analyses revealed that each sponge species possessed a specific microbiota that was significantly different to those of the other species and exhibited attributes that are characteristic of high- and/or lowmicrobial- abundance sponges. These findings emphasize the influence of host identity on the associated microbiota. Dominant sponge- and seawater-associated bacterial phyla were Chloroflexi, Cyanobacteria, and Proteobacteria. Comparison of individual sponge taxa and seawater samples between shallow and deep reef sites revealed no significant variation in alpha diversity estimates, while differences in microbial beta diversity (variation in community composition) were significant for Callyspongia sp. sponges and seawater samples. Overall, the sponge-associated microbiota is significantly shaped by host identity across all samples, while the effect of habitat differentiation seems to be less predominant in tropical reef sponges.

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