Considering the Other Half of the Gut Microbiome: Bacteriophages

ABSTRACT Bacteriophages, viruses specific to bacteria, regulate bacterial communities in all known microbial systems. My research aims to determine how they interact with the trillions of bacteria found in the human gut. To do this, I apply a whole-systems perspective on both communities, considering bacteriophage replication cycles, bacterial and bacteriophage diversity, temporal dynamics, interactions, and responses to perturbations. Building upon ecological concepts and an array of independent and complementary techniques, I study the human gut from a microbial perspective. In contrast with bacteria, working with bacteriophage communities comes with many significant challenges, starting with the limited experimental toolkit and curated databases. Yet an increasing number of studies are pushing these scientific boundaries every day. In the human gut, future research that includes bacteriophages will lead to many exciting and warranted research avenues. From phage therapy and immunization to targeted drug delivery, the sky is the limit in my opinion.

Download Full-text

Modeling the temporal dynamics of cervicovaginal microbiota identifies targets that may promote reproductive health

Microbiome ◽

10.1186/s40168-021-01096-9 ◽

2021 ◽

Vol 9 (1) ◽

Author(s):

Alexander Munoz ◽

Matthew R. Hayward ◽

Seth M. Bloom ◽

Muntsa Rocafort ◽

Sinaye Ngcapu ◽

...

Keyword(s):

High Risk ◽

Bacterial Communities ◽

High Probability ◽

Temporal Dynamics ◽

Transition Probabilities ◽

Low Risk ◽

Sub Saharan Africa ◽

Reproductive Outcomes ◽

Bacterial Composition ◽

Sub Saharan

Abstract Background Cervicovaginal bacterial communities composed of diverse anaerobes with low Lactobacillus abundance are associated with poor reproductive outcomes such as preterm birth, infertility, cervicitis, and risk of sexually transmitted infections (STIs), including human immunodeficiency virus (HIV). Women in sub-Saharan Africa have a higher prevalence of these high-risk bacterial communities when compared to Western populations. However, the transition of cervicovaginal communities between high- and low-risk community states over time is not well described in African populations. Results We profiled the bacterial composition of 316 cervicovaginal swabs collected at 3-month intervals from 88 healthy young Black South African women with a median follow-up of 9 months per participant and developed a Markov-based model of transition dynamics that accurately predicted bacterial composition within a broader cross-sectional cohort. We found that Lactobacillus iners-dominant, but not Lactobacillus crispatus-dominant, communities have a high probability of transitioning to high-risk states. Simulating clinical interventions by manipulating the underlying transition probabilities, our model predicts that the population prevalence of low-risk microbial communities could most effectively be increased by manipulating the movement between L. iners- and L. crispatus-dominant communities. Conclusions The Markov model we present here indicates that L. iners-dominant communities have a high probability of transitioning to higher-risk states. We additionally identify transitions to target to increase the prevalence of L. crispatus-dominant communities. These findings may help guide future intervention strategies targeted at reducing bacteria-associated adverse reproductive outcomes among women living in sub-Saharan Africa.

Download Full-text

Forest Quality Dynamic Change and Its Driving Factors Accompanied by Forest Transition in China

Forests ◽

10.3390/f12060733 ◽

2021 ◽

Vol 12 (6) ◽

pp. 733

Author(s):

Li Gu ◽

Zhiwen Gong ◽

Yuankun Bu

Keyword(s):

Fixed Effects ◽

Temporal Dynamics ◽

Spatial Clustering ◽

Dynamic Change ◽

Forest Area ◽

Future Research ◽

Suitable Model ◽

Forest Transition ◽

Significance Level ◽

Province Level

As ecological and environmental issues have received continuous attention, forest transition has gradually become the frontier and a hot issue, which have implications for biodiversity and ecosystem functioning. In this study, the spatial-temporal dynamics and the spatial determinants of forest quality were investigated using spatial econometric regression models at the province level, which contained 31 provinces, autonomous regions, and municipalities in China. The results showed that forest area, forest volume, forest coverage, and forest quality have greatly increased as of 2018, but uneven forest distribution is an important feature of forest adaptation to the environment. The global Moran’s I value was greater than 0.3, and forest quality of the province level had a positive spatial correlation and exhibited obvious spatial clustering characteristics. In particular, the spatial expansion of forest quality had shown an accelerated concentration. The most suitable model for empirical analysis and interpretation was the Spatial Durbin Model (SDM) with fixed effects. The average annual precipitation and the area ratio of the collective forest were positively correlated with forested quality (significance level 1%). Ultimately, this framework could guide future research, describe actual and potential changes in forest quality associated with forest transitions, and promote management plans that incorporate forest area changes.

Download Full-text

Temporal Dynamics of PERMA Building Blocks and Well-being in Daily Life: An Ecological Momentary Assessment

10.31234/osf.io/gs2vd ◽

2021 ◽

Author(s):

Saeideh Heshmati ◽

Zita Oravecz

Keyword(s):

Ecological Momentary Assessment ◽

Temporal Dynamics ◽

Daily Life ◽

Well Being ◽

Building Blocks ◽

Individual Variability ◽

Future Research ◽

Dynamical Features ◽

Ecological Momentary ◽

Momentary Assessment

Most assessments of well-being have relied on retrospective accounts, measured by global evaluative well-being scales. Following the recent debates focused on the assessment of hedonic and eudaimonic well-being based on the elements of the PERMA theory, the current study aimed to shed further light onto the measurement of PERMA elements in daily life and their temporal dynamics. Through an Ecological Momentary Assessment (EMA) design (N=160), we examined the dynamics of change (e.g., baselines and intra-individual variability) in the PERMA elements using the mPERMA measure, which is an EMA-adapted version of the PERMA Profiler. Findings revealed that momentary experiences of well-being, quantified via PERMA elements, map onto their corresponding hedonic or eudaimonic well-being components, and its dynamical features provide novel insights into predicting global well-being. This work offers avenues for future research to assess well-being in real-time and real-world contexts in ecologically valid ways, while eliminating recall bias.

Download Full-text

Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin

Frontiers in Microbiology ◽

10.3389/fmicb.2016.00476 ◽

2016 ◽

Vol 7 ◽

Cited By ~ 36

Author(s):

Francesco P. Mancuso ◽

Sofie D'Hondt ◽

Anne Willems ◽

Laura Airoldi ◽

Olivier De Clerck

Keyword(s):

Bacterial Communities ◽

Temporal Dynamics ◽

Cystoseira Compressa

Download Full-text

GUIDING FUTURE RESEARCH ON THE VALORISATION OF SHREDDER FINE RESIDUES: A REVIEW OF FOUR DECADES OF RESEARCH

Detritus ◽

10.31025/2611-4135/2019.13868 ◽

2019 ◽

pp. 150-164 ◽

Cited By ~ 1

Author(s):

Tharaka Gunaratne ◽

Joakim Krook ◽

Mats Eklund ◽

Hans Andersson

Keyword(s):

Process Development ◽

Future Research ◽

Research Topics ◽

Main Research ◽

Systems Perspective ◽

Material Characterisation ◽

Micro Level ◽

Substitute Material ◽

The Individual ◽

Contamination Problem

Millions of tonnes of shredder fines are generated and disposed of globally, despite compelling reasons for its recovery. The absence of a review of previous literature, however, makes it difficult to understand the underlying reasons for this. Thus, this study attempts to investigate and assess what, to what extent, and in what ways shredder fines have been addressed in previous research. In doing so, guidelines are drawn for future research to facilitate the valorisation (upgrading and recovery) of shredder fines. Previous research concerning shredder fines was identified with respect to three main research topics. The material characterisation studies are predominantly confined to the occurrence of metals due to their recovery and contamination potential. The process development studies have often undertaken narrowly conceived objectives of addressing one resource opportunity or contamination problem at a time. Consequently, the full recovery (the retrieval of valuable resources and the bulk-utilisation as substitute material) potential of shredder fines has been largely overlooked. The main limitation of policy and regulation studies is the absence of in-depth knowledge on the implications of governmental waste- and resource-policies (macro-level) on actors’ incentives and capacities (micro-level) for fines valorisation, which is necessary to understand the marketability of fines-derived resources. Undertaking a systems perspective is the key to recognising not only the different aspects within the individual research topics but also the inter-relations between them. It also facilitates the internalisation of the inter-relations into topical research.

Download Full-text

The reality of rurality : parent experiences with best start in two rural communities

10.32920/ryerson.14658165.v1 ◽

2021 ◽

Author(s):

Kerri Graham

Keyword(s):

Rural Communities ◽

Service Delivery ◽

Urban Communities ◽

Care Service ◽

Future Research ◽

Systems Perspective ◽

Parent Experiences ◽

Rural And Urban ◽

Challenges And Opportunities ◽

Rural Service Delivery

Human services literature from a variety of disciplines demonstrates that rural and urban communities pose different challenges and opportunities for service delivery; however, little research specifically explores early learning and care service delivery in rural communities. This qualitative study draws on a critical ecological systems perspective to examine the experiences of rural parents accessing services through a specific service delivery strategy, Best Start networks. Thematic analysis was used to analyze data gathered from two rural communities as part of a larger study examining parent experiences with Best Start in three communities across Ontario (Underwood, Killoran, & Webster, 2010). Three themes emerged that related specifically to the rural experience: (a) Opportunities for Social Interaction; (b) Accessibility of Services; and, (c) Impact of Personal Relationships. Results indicate that certain factors related to rural life and location affected parents' experiences with Best Start services. Drawing on the broadly defined concept of accessibility, implications for rural service delivery are discussed and recommendations for practice and future research are presented.

Download Full-text

Host phylogeny drives the structure and diversity of insect microbiota

10.1101/2021.07.19.452888 ◽

2021 ◽

Author(s):

Antonino Malacrino'

Keyword(s):

Bacterial Communities ◽

Management Practices ◽

Life Stage ◽

Future Research ◽

Sequencing Data ◽

Insect Nutrition ◽

Common Framework ◽

Host Phylogeny ◽

Insect Taxonomy ◽

Outstanding Question

Microorganisms have an enormous impact on most of the life that inhabits our planet. Insects are an excellent example, as research showed that several microbial species are essential for insect nutrition, reproduction, fitness, defence and many other functions. More recently, we assisted to an exponential growth of studies describing the taxonomical composition of bacterial communities across insects' phylogeny. However, there is still an outstanding question that needs to be answered: which factors contribute most in shaping insects' microbiomes? This study tries to find an answer to this question by taking advantage of publicly available sequencing data and reanalysing over 4,000 samples of insect-associated bacterial communities under a common framework. Results suggest that insect taxonomy has a wider impact on the structure and diversity of their associated microbial communities than the other factors considered (diet, sex, life stage, sample origin and treatment). Also, a survey of the literature highlights several methodological limitations that needs to be considered in future research endeavours. This study proofs the amount of collective effort that lead to the current understanding of insect-microbiota interactions and their influence on insect biology, ecology and evolution with potential impact on insect conservation and management practices.

Download Full-text

An Accounting Information Systems Perspective on Data Analytics and Big Data

Journal of Information Systems ◽

10.2308/isys-51799 ◽

2017 ◽

Vol 31 (3) ◽

pp. 101-114 ◽

Cited By ~ 19

Author(s):

Esperanza Huerta ◽

Scott Jensen

Keyword(s):

Big Data ◽

Information Systems ◽

Data Analytics ◽

Accounting Information ◽

Security Requirements ◽

Future Research ◽

Accounting Information Systems ◽

Systems Perspective ◽

Analytic Skills

ABSTRACT Forty-six academics and practitioners participated in the second Journal of Information Systems Conference to discuss data analytics and Big Data from an accounting information systems perspective. The panels discussed the evolving role of technology in accounting, privacy within the domain of Big Data, and people and Big Data. Throughout all three panels, several topics emerged that impact all areas of accounting—developing enhanced analytical and data handling skills; evaluating privacy, security requirements, and risks; thinking creatively; and assessing the threat of automation to the accounting profession. Other topics were specific to a segment of the profession, such as the growing demand for privacy compliance audits and the curriculum adjustments necessary to develop data analytic skills. This commentary synthesizes and expands the discussions of the conference panels and suggests potential areas for future research.

Download Full-text