Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework

Wasimuddin, Wasimuddin; Schlaeppi, Klaus; Ronchi, Francesca; Leib, Stephen L.; Erb, Matthias; Ramette, Alban

doi:10.1101/843144

Cited by 11 publications

(8 citation statements)

References 49 publications

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“…S2). These values are well within the range of archaeal relative abundance estimates quantified with catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH) (Lloyd et al 2013), likely because V4 primers may not discriminate strongly against archaea (Wasimuddin et al 2019). Bacteria to archaea ratios, in particular those of the surface sediments at the deep stations (2.7±0.4, Fig.…”

supporting

confidence: 63%

Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

Rubin‐Blum

Sisma-Ventura

Yudkovski

et al. 2021

Preprint

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Microbes are key players in marine sediments, yet they are not accessed routinely by monitoring programs. Here, we investigate the spatial and vertical trends in the abundance, activity and diversity of benthic archaea, bacteria and fungi of the southeastern Mediterranean Sea (SEMS), based on ∼150 samples collected by the National Monitoring Program in 2018-2020 in coastal, as well as deep-sea transects across the Israeli exclusive economic zone, using vertical profiles of short sediment cores (0-1, 1-2, 4-5, 9-10 and 19-20 cm below surface). Microbial abundance was usually low (0.01 ×108 to 0.21×108 cells gr-1 sediment), while heterotrophic productivity was the highest in the nearshore stations (12±4 ng C gr-1 sediment h-1), as opposed to 0.5±0.9 ng C gr-1 sediment h-1 at the offshore sites. Using amplicon sequencing of marker genes, we identified the changes in the diversity of microbes along environmental gradients, in the four dimensions (geographic location, seabed depth, distance from the sediment surface and time). We show high taxonomic diversity of bacteria and archaea (Shannon’s H’ 5.0-6.9) and lesser diversity of fungi (Shannon’s H’ 0.2-4.8). We use DESeq2 analyses to highlight the role of ammonia-oxidizing Nitrososphaeria in the aerated sediments of the continental slope and deep bathyal plain stations and organotrophic lineages in coastal, shelf, slope, and abyssal plain sediments. Based on taxonomic diversity, we infer the metabolic potential of these communities. Analyses of fungi diversity and guilds suggest the prevalence of the saprotrophic and pathotrophic microfungi Ascomycota (70±23%) and Basidiomycota (16±18%) in the SEMS sediments. We provide a comprehensive baseline of benthic microbial populations in the SEMS and pledge for the use of microbial indices in biomonitoring of the marine environment.

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supporting

confidence: 63%

Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

Rubin‐Blum

Sisma-Ventura

Yudkovski

et al. 2021

Preprint

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“…3A). The primer pair used in this study can also amplify archaea (Wasimuddin et al, 2020) and we found Crenarchaeota and Euryarchaeota in Tomba degli Scudi (Fig. 3A).…”

Section: Subterranean Tombs That Are Highly Permissive For Lifementioning

confidence: 75%

Active microbial ecosystem in Iron‐Age tombs of the Etruscan civilization

Cirigliano

Mura

Cecchini³

et al. 2020

Environmental Microbiology

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Earth's microbial biosphere extends down through the crust and much of the subsurface, including those microbial ecosystems located within cave systems. Here, we elucidate the microbial ecosystems within anthropogenic 'caves'; the Iron-Age, subterranean tombs of central Italy. The interior walls of the rock (calcium-rich macco) were painted 2500 years ago and are covered with CaCO 3 needles (known as moonmilk). The aims of the current study were to: identify biological/geochemical/biophysical determinants of and characterize bacterial communities involved in CaCO 3 precipitation; challenge the maxim that biogenic activity necessarily degrades surfaces; locate the bacterial cells that are the source of the CaCO 3 precipitate; and gain insight into the kinetics of moonmilk formation. We reveal that this environment hosts communities that consist primarily of bacteria that are mesophilic for temperature and xerotolerance (including Actinobacteria, Bacteroidetes and Proteobacteria); is populated by photosynthetic Cyanobacteria exhibiting heterotrophic nutrition (Calothrix and Chroococcidiopsis); and has CaCO 3 precipitating on the rock surfaces (confirmation that this process is biogenic) that acts to preserve rather than damage the painted surface. We also identified that some community members are psychrotolerant (Polaromonas), acidotolerant or acidophilic (members of the Acidobacteria), or resistant to ionizing radiation (Brevundimonas and Truepera); elucidate the ways in which microbiology impacts mineralogy and vice versa; and reveal that biogenic formation of moonmilk can occur rapidly, that is, over a period of 10 to 56 years. We discuss the paradox that these ecosystems, that are for the most part in the dark and lack primary production, are apparently highly active, biodiverse and biomass-rich.

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“…These primers have been demonstrated to perform well for characterising the gut microbiota, however efficacy/performance for characterisation of the oral microbiota requires further investigation. A recent study showed a discrepancy in performance when applied to human gut versus skin microbiota [37]. Most studies of the saliva microbiota have employed primers which target the V2 variable region.…”

Section: Discussionmentioning

confidence: 99%

Influential factors of saliva microbiota composition

Wells

Sprockett

Bowyer

et al. 2021

Preprint

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Background: The oral microbiota is emerging as an influential factor of host physiology and disease state. Factors influencing oral microbiota composition have not been well characterised. In particular, there is a lack of population-based studies. We undertook a large hypothesis-free study of the saliva microbiota, considering potential influential factors of host health (frailty; diet; periodontal disease), demographics (age; sex; BMI) and sample processing (storage time), in a sample (n=679) of the TwinsUK cohort of adult twins. Results: Alpha and beta diversity of the saliva microbiota was associated most strongly with frailty (alpha diversity: Q = 0.003, Observed; Q=0.002, Shannon; Q=0.003, Simpson; Beta diversity: Q = 0.002, Bray Curtis dissimilarity ) and age (alpha diversity: Q=0.006, Shannon; Q=0.003, Simpson; beta diversity: Q=0.002, Bray Curtis dissimilarity; Q= 0.032, Weighted UniFrac) in multivariate models including age, frailty, sex, BMI, frailty and diet, and adjustment for multiple testing. Those with a more advanced age were more likely to be dissimilar in the saliva microbiota composition than younger participants (P = 5.125e-06, ANOVA). In subsample analyses, including consideration of periodontal disease (total n=138, periodontal disease n=66), the association with frailty remained for alpha diversity (Q=0.002, Observed ASVs; Q= 0.04 Shannon Index), but not beta diversity, whilst age was not demonstrated to associate with alpha or beta diversity in this subsample, potentially due to insufficient statistical power. Length of time that samples were stored prior to sequencing was associated with beta diversity (Q = 0.002, Bray Curtis dissimilarity). Six bacterial taxa were associated with age after adjustment for frailty and diet. Conclusions: Frailty and age emerged as the most influential factors of saliva microbiota composition. Whilst frailty and age are correlates, the associations were independent of each other, suggesting that both biological and chronological ageing are key drivers of saliva microbiota composition.

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Evaluation of primer pairs for microbiome profiling across a food chain from soils to humans within the One Health framework

Cited by 11 publications

References 49 publications

Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

Diversity, activity and abundance of benthic microbes in the southeastern Mediterranean Sea: A baseline for monitoring

Active microbial ecosystem in Iron‐Age tombs of the Etruscan civilization

Influential factors of saliva microbiota composition

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