Biology subjects

Gobbi, A.

Publications and source records attributed to Gobbi, A..

9 recordsLinked to original sources

bioRxiv2024

Binning meets taxonomy: TaxVAMB improves metagenome binning using bi-modal variational autoencoder

A common procedure for studying the microbiome is binning the sequenced contigs into metagenome-assembled genomes. Currently, unsupervised and self-supervised deep learning based methods using co-abundance and sequence based motifs such as tetranucleotide frequencies are state-of-the-art for metagenome binning. Taxonomic labels derived from alignment based classification have not been widely used. Here, we propose TaxVAMB, a metagenome binning tool based on semi-supervised bi-modal variational autoencoders, combining tetranucleotide frequencies and contig co-abundances with contig annotations returned by any taxonomic classifier on any taxonomic rank. TaxVAMB outperforms all other binners on CAMI2 human microbiome datasets, returning on average 40% more near-complete assemblies than the next best binner. On real long-read datasets TaxVAMB recovers on average 13% more near-complete bins and 14% more species. When used in a single-sample setup, TaxVAMB on average returns 83% more high quality bins than VAMB. TaxVAMB bins incomplete genomes drastically better than any other tool, returning 255% more high quality bins of incomplete genomes than the next best binner. Our method has immediate research and industrial applications, as well as methodological novelty which can be translated to other biological problems with semi-supervised multimodal datasets.

bioinformatics↗

bioRxiv2024

A single strand-based library preparation method for unbiased virome characterization

The gut virome is an integral component of the gut microbiome, playing a crucial role in maintaining gut health. However, accurately depicting the entire gut virome is challenging due to the inherent limitations and biases associated with current sequencing library preparation methods. To overcome these problems, we repurposed the ligation-based single-stranded library (SSLR) preparation method for virome studies. We demonstrate that the SSLR method exhibits exceptional efficiency in quantifying viral DNA genomes (both dsDNA and ssDNA) and outperforms existing double-stranded (Nextera) and single-stranded (xGen, MDA+Nextera) library preparation approaches in terms of minimal amplification bias, evenness of coverage, and integrity of assembling viral genomes. The SSLR method can be utilized for the simultaneous library preparation of both DNA and RNA viral genomes. Furthermore, the SSLR method showed its ability to capture highly modified phage genomes, which were often lost using other library preparation approaches.

microbiology↗

bioRxiv2023

The effect of colonic pH on microbial activity and metabolite production using common prebiotics as substrates: an in vitro study

The interplay between gut microbiota (GM) and host via degradation of dietary components leading to the production of metabolites such as short-chain fatty acids (SCFAs) is affected by a range of factors including colonic pH and carbohydrate source. Here we investigate how differences in colonic pH influence GM composition and metabolite production using different substrates including inulin, lactose, Galactooligosaccharides (GOS), and Fructooligosaccharide (FOS) in an in vitro colon setup. We investigated 3 different pH regimes (low, 5.2 increasing to 6.4; medium, 5.6 increasing to 6.8 and high, 6.0 increasing to 7.2) and found that Bacteroides spp. decreased but Bifidobacterium spp. became abundant under low pH regimes, suggesting complex interactions of the bacterial community in the face of pH fluctuations in the colon. The butyrate producers Butyricimonas and Christensenella were enriched at higher pH conditions, where also butyrate production was increased using inulin as substrate. The relative abundance of Phascolarctobacterium, Bacteroides, and Rikenellaceae was also increased at higher colonic pH, which was accompanied by increased production of propionate using GOS and FOS as substrate. The gastrointestinal factors are linked in a complex network, where microbial activity leads to the production of SCFAs and other compounds that influence pH, which in turn seems to influence microbial activity. Taken together, our results show that dynamic changes in colonic pH under in vitro simulated conditions have a strong effect on gut microbial activity with SCFA production being higher at colonic pH conditions close to neutral.

microbiology↗

bioRxiv2022

Dietary non-starch polysaccharides impair immunity to enteric nematode infection

The influence of diet on immune function and resistance to enteric infection and disease is becoming ever more established. Highly processed, refined diets can lead to inflammation and gut microbiome dysbiosis, whilst health-promoting dietary components such as phytonutrients and fermentable fibres are thought to promote a healthy microbiome and balanced mucosal immunity. Chicory (Cichorium intybus) is a leafy green vegetable rich in fibres and bioactive compounds that may promote gut health. Unexpectedly, we here show that incorporation of chicory into semisynthetic AIN93G diets renders mice susceptible to infection with enteric helminths. Mice fed a high level of chicory leaves (10% dry matter) had a more diverse gut microbiota, but a diminished type-2 immune response to infection with the intestinal roundworm Heligmosomoides polygyrus. Furthermore, the chicory-supplemented diet significantly increased burdens of the caecum-dwelling whipworm Trichuris muris, concomitant with a highly skewed type-1 immune environment in caecal tissue. The chicory-supplemented diet was rich in non-starch polysaccharides, particularly uronic acids (the monomeric constituents of pectin). In accordance, mice fed pectin-supplemented AIN93G diets had higher T. muris burdens and reduced IgE production and expression of genes involved in type-2 immunity. Importantly, treatment of pectin-fed mice with exogenous IL-25 restored type-2 responses and was sufficient to allow T. muris expulsion. Collectively, our data suggest that increasing levels of fermentable, non-starch polysaccharides in refined diets compromises immunity to helminth infection in mice. This diet-infection interaction may inform new strategies for manipulating the gut environment to promote resistance to enteric parasites.

immunology↗

bioRxiv2021

Viruses roam the wheat phyllosphere

The phyllosphere comprises all the above-ground sections of plants. This niche is colonised by complex microbial communities, including algae, fungi, archaea, and bacteria1-3. They are known to induce plant growth and promote health4,5 or act as causative agents of plant diseases6-8. It is thought that the most abundant organisms are phyllobacteria2, with an estimate between 106 to 107 cells per cm2. Viruses are highly abundant across many environments, often outnumbering bacteria 10 to 19. However, not much is known about their abundance and composition in the phyllosphere, a harsh environment for viruses due to environmental variability and high UV exposure. To investigate this niche in detail, we extracted, sequenced and analysed phyllosphere virome. Using leaf samples from winter wheat (Triticum aestivum), we identified a total of 876 viral populations (vOTUs), mostly belonging to the Caudovirales order. Most of these were predicted to be lytic. Remarkably, 810 of these viral populations correspond to new viral species with no matches to known sequences. We estimate a minimum of 2.0 x106 viral particles per leaf. Overall, these findings suggest that the phyllosphere ecosystem harbours an abundant and active community of novel viruses that play essential roles in shaping this habitat.

microbiology↗

bioRxiv2020

Microbial map of the world's vineyards:Applying the concept of microbial terroir on a global scale

The specific microbial biodiversity linked to a particular vineyard location is reported to be a crucial aspect, in conjunction with edaphic, climatic and human factors, in the concept of wine terroir. These biogeographical patterns are known as microbial terroirs. This study applied an HTS amplicon library approach in order to conduct a global survey of vineyards soil microbial communities. In all, soil samples from 200 vineyards on four continents were analysed in an attempt to establish the basis for the development of a vineyard soil microbiome map to represent microbial wine terroirs on a global scale. This study established links between vineyard locations and microbial biodiversity on different scales: between continents and countries, and between different wine regions within the same country. Geography had a strong effect on the composition of microbial communities on a global scale, which was also maintained on a country scale. Furthermore, a predictive model was developed, based on random forest analyses, to discriminate between microbial patterns in order to identify the geographical source of the samples with reasonable precision. Finally this study is the first to describe the microbial community of new and northern wine-producing regions, such as Denmark, that could be of great interest for viticulture adaptation in a context of climate change.

microbiology↗

bioRxiv2020

Bioaugmented sand filter columns provide stable removal of pesticide residue from membrane retentate

Drinking water resources, such as groundwater, are threatened by pollution. The pesticide metabolite 2,6-dichlorobenzamide (BAM) is one of the compounds frequently found in groundwater. Studies have attempted to add specific BAM-degrading bacteria to sand-filters at drinking water treatment facilities. This biotechnology has shown great potential in removing BAM from contaminated water. However, the degradation potential was formerly lost after approximately 2-3 weeks due to a decrease of the degrader population over time. The aim of the present study was to overcome the constraints leading to loss of degraders from inoculated filters. Our approach was threefold: 1) Development of a novel inoculation strategy, 2) lowering the flowrate to reduce washout of cells, and 3) increasing the concentration of nutrients hereunder the pollutant in a smaller inlet water stream. The two latter were achieved via modifications of the inlet water by applying membrane treatment which, besides producing an ultra-pure water fraction, produced a residual water stream with nutrients including BAM concentrated in an approximately 10-fold reduced volume. This was done to alleviate starvation of degrader bacteria in the otherwise oligotrophic sand-filters and to enable a decreased flowrate. By this approach, we achieved 100% BAM removal over a period of 40 days in sand-filter columns inoculated with the BAM-degrader Aminobacter sp. MSH1. Molecular targeting of the degrader strain showed that the population of degrader bacteria persisted at high numbers throughout the sand-filter columns and over the entire timespan of the experiment. 16S rRNA gene amplicon sequencing confirmed that MSH1 dominated the bacterial communities. IMPORTANCEMany countries rely partly or solely on groundwater as the source of drinking water. Here groundwater contamination by pesticide residues poses a serious threat to the production of high quality drinking water. Since scarcity of clean groundwater may occur in progressively larger areas both locally and globally, the need for efficient purification technologies is growing. This study shows that a novel system combining membrane treatment and bioaugmented sand-filters can efficiently remove pesticide residues in laboratory columns when applying specific inoculation and flow conditions. Once upscaled, this system can be used directly for pump-and-treat of contaminated groundwater wells or at drinking water treatment plants.

microbiology↗

bioRxiv2019

Seasonal microbial dynamics on grapevine leaves under biocontrol and copper fungicide treatments

Winemakers have long used copper as a fungicide on grapevine. However, the potential of copper to accumulate on soil and affect the biota poses a challenge to achieving sustainable agriculture. One recently developed option is the use of biocontrol agents to replace or complement traditional methods. In the present study, a field experiment was conducted in South Africa in which the leaves in two blocks of a vineyard were periodically treated with either copper sulphate or sprayed with Lactobacillus plantarum MW-1 as a biocontrol agent. This study evaluated the impact of the two treatments on the bacterial and fungal communities as they changed during the growing season. To do this, NGS was combined with quantitative strain-specific and community qPCRs. The results revealed the progression of the microbial communities throughout the season and how the different treatments affected the microbiota. Bacteria appeared to be relatively stable at the different time points, with the only taxa that systematically changed between treatments being Lactobacillaceae, which included reads from the biocontrol agent. Cells of Lactobacillus plantarum MW-1 were only detected on treated leaves using strain-specific qPCR, with its amount spanning from 103to 105cells/leaves. Conversely the fungal community was largely shaped by a succession of different dominant taxa over the months. Between treatments, only a few fungal taxa appeared to change significantly and the number of ITS copies was also comparable. In this regards, the two treatments seemed to affect the microbial community similarly, revealing the potential of this biocontrol strain as a promising alternative among sustainable fungicide treatments, although further investigation is required.

microbiology↗

bioRxiv2018

Quantitative and qualitative evaluation of the impact of the G2 enhancer, bead sizes and lysing tubes on the bacterial community composition during DNA extraction from recalcitrant soil core samples based on community sequencing and qPCR

Soil DNA extraction encounters numerous challenges that can affect both yield and purity of the recovered DNA. Clay particles lead to reduced DNA extraction efficiency, and PCR inhibitors from the soil matrix can negatively affect downstream analyses when applying DNA sequencing. Further, these effects impede molecular analysis of bacterial community compositions in lower biomass samples, as often observed in deeper soil layers. Many studies avoid these complications by using indirect DNA extraction with prior separation of the cells from the matrix, but such methods introduce other biases that influence the resulting microbial community composition.\n\nTo address these issues, a direct DNA extraction method was applied in combination with the use of a commercial product, the G2 DNA/RNA Enhancer(R), marketed as being capable of improving the amount of DNA recovered after the lysis step. The results showed that application of G2 increased DNA yields from the studied clayey soils from layers between 1.00 and 2.20 m below ground level.\n\nImportantly, the use of G2 did not introduce bias, as it did not result in any significant differences in the biodiversity of the bacterial community measured in terms of alpha and beta diversity and taxonomical composition.\n\nFinally, this study considered a set of customised lysing tubes for evaluating possible influences on the DNA yield. Tubes customization included different bead sizes and amounts, along with lysing tubes coming from two suppliers. Results showed that the lysing tubes with mixed beads allowed greater DNA recovery compared to the use of either 0.1 or 1.4 mm beads, irrespective of the tube supplier.\n\nThese outcomes may help to improve commercial products in DNA/RNA extraction kits, besides raising awareness about the optimal choice of additives, offering opportunities for acquiring a better understanding of topics such as vertical microbial characterisation and environmental DNA recovery in low biomass samples.

microbiology↗