Exploring clade differentiation of the Faecalibacterium prausnitzii complex

Faecalibacterium prausnitzii is one of the most prevalent and abundant polyphyletic health18 promoting components of the human gut microbiome with a propensity for dysbiotic decreases. To better understand its biology in the human gut, we specifically explored the divergence pressures acting on F. prausnitzii clades on a global scale. Five F. prausnitzii clades were de novo identified from 55 publicly available genomes and 92 high-quality metagenome assembled genomes. Divergence rate indices were constructed and validated to compare the divergence rates among the different clades and between each of the diverging genes. For each clade we identified specific patterns of diverging functionalities, probably reflecting different ecological propensities, in term of inter-host dispersion capacity or exploitation of different substrates in the gut environment. Finally, we speculate that these differences may explain, at least in part, the observed differences in the overall divergence rates of F. prausnitzii clades in human populations

Metagenomic trajectory of gut microbiome in the human lifespan

Co-evolving with the human host, gut microbiota establishes configurations, which vary under the pressure of inflammation, disease, ageing, diet and lifestyle. In order to describe the multi-stability of the microbiome-host relationship, we studied specific tracts of the bacterial trajectory during the human lifespan and we characterized peculiar deviations from the hypothetical development, caused by disease, using molecular techniques, such as phylogenetic microarray and next-generation sequencing. Firstly, we characterized the enterocyte-associated microbiota in breast-fed infants and adults, describing remarkable differences between the two groups of subjects. Successively, we investigated the impact of atopy on the development of the microbiome in Italian childrens, highlithing conspicuous deviations from the child-type microbiota of the Italian controls. To explore variation in the gut microbiota depending on geographical origins, which reflect different lifestyles, we compared the phylogenetic diversity of the intestinal microbiota of the Hadza hunter-gatherers of Tanzania and Italian adults. Additionally, we characterized the aged-type microbiome, describing the changes occurred in the metabolic potential of the gut microbiota of centenarians with respect to younger individuals, as a part of the pathophysiolology of the ageing process. Finally, we evaluated the impact of a probiotics intervention on the intestinal microbiota of elderly people, showing the repair of some age-related dysbioses. These studies contribute to elucidate several aspects of the intestinal microbiome development during the human lifespan, depicting the microbiota as an extremely plastic entity, capable of being reconfigured in response to different environmental factors and/or stressors of endogenous origin

Connect the dots: sketching out microbiome interactions through networking approaches

Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment

An evaluation of faculty development programme on the design and development of self-learning materials for open distance learning

Purpose – This paper seeks to ascertain the effectiveness of a two-week-long faculty development programme (FDP), organized by Indira Gandhi National Open University (IGNOU), for teachers of the open and distance learning (ODL) system, with the aim of upgrading their knowledge and skills for developing print self-learning materials (SLMs). The specific aim of this study is to ascertain whether the objectives of the FDP have been achieved, to examine the effectiveness of the training programme and to suggest measures for improvement in future FDPs regarding the design and development of print SLMs. Design/methodology/approach – The study was conducted using a descriptive survey research method, through semi-structured questionnaires and adopted purposive sampling. The first survey was conducted immediately after the completion of the programme, in order to collect feedback from the trainees, while the second survey was conducted after six months of the FDP, using the follow-up approach, so that more reliable and authentic results could be obtained. Findings – The outcomes of the study revealed that the training had been effective in imparting appropriate knowledge and skills to the trainees, with respect to designing print SLMs. However, certain gaps were also identified and have been reported in this paper. Key suggestions have been made to address the shortcomings and improve forthcoming FDPs. Research limitations/implications – The present research focused on a specific training programme regarding the design and development of SLMs. Therefore, only the teachers and academics who participated in this specialized training activity were considered for the collection of feedback. Practical implications – The recommendations of this work may be useful for the trainers, FDP coordinators, training institutions and ODL policymakers for planning and designing effective staff development activities for teachers and academics working in ODL institutions. These would be especially useful in the design of FDPs, aimed at orienting teachers who are involved in curriculum planning, design and development of learning resources. Originality/value – This study is an original research based on the empirical primary data obtained by the researchers. As the largest open university in the world, IGNOU has been playing a key role in staff development for and in ODL in developing countries. This evaluative study of a specialized FDP in the area of SLM design and development is a significant work that may be valuable for planning the staff development strategies and building a training evaluation mechanism

G2S: A New Deep Learning Tool for Predicting Stool Microbiome Structure From Oral Microbiome Data

Deep learning methodologies have revolutionized prediction in many fields and show the potential to do the same in microbial metagenomics. However, deep learning is still unexplored in the field of microbiology, with only a few software designed to work with microbiome data. Within the meta-community theory, we foresee new perspectives for the development and application of deep learning algorithms in the field of the human microbiome. In this context, we developed G2S, a bioinformatic tool for taxonomic prediction of the human fecal microbiome directly from the oral microbiome data of the same individual. The tool uses a deep convolutional neural network trained on paired oral and fecal samples from populations across the globe, which allows inferring the stool microbiome at the family level more accurately than other available approaches. The tool can be used in retrospective studies, where fecal sampling was not performed, and especially in the field of paleomicrobiology, as a unique opportunity to recover data related to ancient gut microbiome configurations. G2S was validated on already characterized oral and fecal sample pairs, and then applied to ancient microbiome data from dental calculi, to derive putative intestinal components in medieval subjects

HumanMycobiomeScan: A new bioinformatics tool for the characterization of the fungal fraction in metagenomic samples

Background: Modern metagenomic analysis of complex microbial communities produces large amounts of sequence data containing information on the microbiome in terms of bacterial, archaeal, viral and eukaryotic composition. The bioinformatics tools available are mainly devoted to profiling the bacterial and viral fractions and only a few software packages consider fungi. As the human fungal microbiome (human mycobiome) can play an important role in the onset and progression of diseases, a comprehensive description of host-microbiota interactions cannot ignore this component. Results: HumanMycobiomeScan is a bioinformatics tool for the taxonomic profiling of the mycobiome directly from raw data of next-generation sequencing. The tool uses hierarchical databases of fungi in order to unambiguously assign reads to fungal species more accurately and > 10,000 times faster than other comparable approaches. HumanMycobiomeScan was validated using in silico generated synthetic communities and then applied to metagenomic data, to characterize the intestinal fungal components in subjects adhering to different subsistence strategies. Conclusions: Although blind to unknown species, HumanMycobiomeScan allows the characterization of the fungal fraction of complex microbial ecosystems with good performance in terms of sample denoising from reads belonging to other microorganisms. HumanMycobiomeScan is most appropriate for well-studied microbiomes, for which most of the fungal species have been fully sequenced. This released version is functionally implemented to work with human-associated microbiota samples. In combination with other microbial profiling tools, HumanMycobiomeScan is a frugal and efficient tool for comprehensive characterization of microbial ecosystems through shotgun metagenomics sequencing

Theatre is a valid add-on therapeutic intervention for emotional rehabilitation of parkinson's disease patients

Conventional medical treatments of Parkinson's disease (PD) are effective on motor disturbances but may have little impact on nonmotor symptoms, especially psychiatric ones. Thus, even when motor symptomatology improves, patients might experience deterioration in their quality of life. We have shown that 3 years of active theatre is a valid complementary intervention for PD as it significantly improves the well-being of patients in comparison to patients undergoing conventional physiotherapy. Our aim was to replicate these findings while improving the efficacy of the treatment. We ran a single-blinded pilot study lasting 15 months on 24 subjects with moderate idiopathic PD. 12 were assigned to a theatre program in which patients underwent "emotional" training. The other 12 underwent group physiotherapy. Patients were evaluated at the beginning and at the end of their treatments, using a battery of eight clinical and five neuropsychological scales. We found that the emotional theatre training improved the emotional well-being of patients, whereas physiotherapy did not. Interestingly, neither of the groups showed improvements in either motor symptoms or cognitive abilities tested by the neuropsychological battery. We confirmed that theatre therapy might be helpful in improving emotional well-being in PD

Gut microbiome response to a modern Paleolithic diet in a Western lifestyle context

The modern Paleolithic diet (MPD), featured by the consumption of vegetables, fruit, nuts, seeds, eggs, fish and lean meat, while excluding grains, dairy products, salt and refined sugar, has gained substantial public attention in recent years because of its potential multiple health benefits. However, to date little is known about the actual impact of this dietary pattern on the gut microbiome (GM) and its implications for human health. In the current scenario where Western diets, low in fiber while rich in industrialized and processed foods, are considered one of the leading causes of maladaptive GM changes along human evolution, likely contributing to the increasing incidence of chronic non-communicable diseases, we hypothesize that the MPD could modulate the Western GM towards a more “ancestral” configuration. In an attempt to shed light on this, here we profiled the GM structure of urban Italian subjects adhering to the MPD, and compared data with other urban Italians following a Mediterranean Diet (MD), as well as worldwide traditional hunter-gatherer populations from previous publications. Notwithstanding a strong geography effect on the GM structure, our results show an unexpectedly high degree of biodiversity in MPD subjects, which well approximates that of traditional populations. The GM of MPD individuals also shows some peculiarities, including a high relative abundance of bile-tolerant and fat-loving microorganisms. The consumption of plant-based foods–albeit with the exclusion of grains and pulses–along with the minimization of the intake of processed foods, both hallmarks of the MPD, could therefore contribute to partially rewild the GM but caution should be taken in adhering to this dietary pattern in the long term

Microbiome network in the pelagic and benthic offshore systems of the northern Adriatic Sea (Mediterranean Sea)

Because of their recognized global importance, there is now the urgent need to map diversity and distribution patterns of marine microbial communities. Even if available studies provided some advances in the understanding the biogeographical patterns of marine microbiomes at the global scale, their degree of plasticity at the local scale it is still underexplored, and functional implications still need to be dissected. In this scenario here we provide a synoptical study on the microbiomes of the water column and surface sediments from 19 sites in a 130 km2 area located 13.5 km afar from the coast in the North-Western Adriatic Sea (Italy), providing the finest-scale mapping of marine microbiomes in the Mediterranean Sea. Pelagic and benthic microbiomes in the study area showed sector specific-patterns and distinct assemblage structures, corresponding to specific variations in the microbiome network structure. While maintaining a balanced structure in terms of potential ecosystem services (e.g., hydrocarbon degradation and nutrient cycling), sector-specific patterns of over-abundant modules-and taxa-were defined, with the South sector (the closest to the coast) characterized by microbial groups of terrestrial origins, both in the pelagic and the benthic realms. By the granular assessment of the marine microbiome changes at the local scale, we have been able to describe, to our knowledge at the first time, the integration of terrestrial microorganisms in the marine microbiome networks, as a possible natural process characterizing eutrophic coastal area. This raises the question about the biological threshold for terrestrial microorganisms to be admitted in the marine microbiome networks, without altering the ecological balance

Seasonal Changes in Microbial Communities Associated With the Jewel Anemone Corynactis viridis.

Increasing evidence indicates that host-associated microbial communities play a key role in the biology of marine eukaryotic organisms. Amongst them, Corallimorpharia are extensively found on reefs, carpeting vast reef areas, where they can exert important roles as habitat forming holobionts, being at the base of complex trophic webs. Here we explore the bacterial community structure, and its changes across different seasons, associated with the jewel anemone Corynactis viridis, an anthozoan Cnidaria that is widely distributed in the northeastern Atlantic Ocean and the Mediterranean Sea. Samples were collected in the North Adriatic Sea in three seasons and the community composition was studied using 16S rDNA sequencing. We show that C. viridis-associated microbial communities are unique and significantly different from those in the surrounding seawater. Interestingly, we observe remarkable changes in the C. viridis microbiome according to seasonality. In particular, the C. viridis microbiome is capable of rearranging its overall ecological structure with the winter-summer transition, moving from an oligotrophic anaerobic community to a heterotrophic ecosystem, with the propensity to ferment proteins and complex polysaccharides. Our findings demonstrate that C. viridis has a unique associated microbiota and suggest that this is capable of adapting to seasonal changes in the host physiology, by establishing a microbiome-host interaction process whose relevance to C. viridis has yet to be determined