scholarly journals BEEM-Static: Accurate inference of ecological interactions from cross-sectional metagenomic data

2020 ◽  
Author(s):  
Chenhao Li ◽  
Tamar V. Av-Shalom ◽  
Jun Wei Gerald Tan ◽  
Junmei Samantha Kwah ◽  
Kern Rei Chng ◽  
...  
Keyword(s):  
Ecological Model ◽  
Expectation Maximization Algorithm ◽  
Microbial Interactions ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Ecological Interactions ◽  
Cross Sectional ◽  
Key Species ◽  
Alternate Model ◽  
And Function

AbstractMotivationThe structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of metagenomic sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional metagenomic datasets for unravelling ecological structure in a scalable manner thus remains an open problem.MethodsWe present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples.ResultsBenchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n=4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species.ConclusionBEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of metagenomic data.

scholarly journals BEEM-Static: Accurate inference of ecological interactions from cross-sectional microbiome data

2021 ◽  
Vol 17 (9) ◽  
pp. e1009343
Author(s):  
Chenhao Li ◽  
Tamar V. Av-Shalom ◽  
Jun Wei Gerald Tan ◽  
Junmei Samantha Kwah ◽  
Kern Rei Chng ◽  
...  
Keyword(s):  
Ecological Model ◽  
Expectation Maximization Algorithm ◽  
Microbial Interactions ◽  
Ecological Interactions ◽  
Cross Sectional ◽  
Key Species ◽  
Alternate Model ◽  
High Fraction ◽  
And Function ◽  
Microbiome Data

The structure and function of diverse microbial communities is underpinned by ecological interactions that remain uncharacterized. With rapid adoption of next-generation sequencing for studying microbiomes, data-driven inference of microbial interactions based on abundance correlations is widely used, but with the drawback that ecological interpretations may not be possible. Leveraging cross-sectional microbiome datasets for unravelling ecological structure in a scalable manner thus remains an open problem. We present an expectation-maximization algorithm (BEEM-Static) that can be applied to cross-sectional datasets to infer interaction networks based on an ecological model (generalized Lotka-Volterra). The method exhibits robustness to violations in model assumptions by using statistical filters to identify and remove corresponding samples. Benchmarking against 10 state-of-the-art correlation based methods showed that BEEM-Static can infer presence and directionality of ecological interactions even with relative abundance data (AUC-ROC>0.85), a task that other methods struggle with (AUC-ROC<0.63). In addition, BEEM-Static can tolerate a high fraction of samples (up to 40%) being not at steady state or coming from an alternate model. Applying BEEM-Static to a large public dataset of human gut microbiomes (n = 4,617) identified multiple stable equilibria that better reflect ecological enterotypes with distinct carrying capacities and interactions for key species. Conclusion BEEM-Static provides new opportunities for mining ecologically interpretable interactions and systems insights from the growing corpus of microbiome data.

scholarly journals Proxi: a Python package for proximity network inference from metagenomic data

2018 ◽  
Author(s):  
Yasser EL-Manzalawy
Keyword(s):  
Network Inference ◽  
Nearest Neighbor ◽  
Microbial Interactions ◽  
Supplementary Information ◽  
Metagenomic Data ◽  
Metagenomic Sequencing ◽  
Proximity Graphs ◽  
Link Type ◽  
Technological Advances ◽  
Python Package

AbstractSummary: Recent technological advances in high-throughput metagenomic sequencing have provided unique opportunities for studying the diversity and dynamics of microbial communities under different health or environmental conditions. Graph-based representation of metagenomic data is a promising direction not only for analyzing microbial interactions but also for a broad range of machine learning tasks including feature selection, classification, clustering, anomaly detection, and dimensionality reduction. We present Proxi, an open source Python package for learning different types of proximity graphs from metagenomic data. Currently, three types of proximity graphs are supported: k-nearest neighbor (k-NN) graphs; radius-nearest neighbor (r-NN) graphs; and perturbed k-nearest neighbor (pk-NN) graphs.Availability: Proxi Python source code is freely available at https://bitbucket.org/idsrlab/proxi/.Contact:[email protected] information: Tutorials and online documentation are available at https://proxi.readthedocs.io

What Is Metagenomics Teaching Us, and What Is Missed?

2020 ◽  
Vol 74 (1) ◽  
pp. 117-135 ◽  
Author(s):  
Felicia N. New ◽  
Ilana L. Brito
Keyword(s):  
Environmental Sustainability ◽  
Metagenomic Data ◽  
Model Organisms ◽  
Metagenomic Sequencing ◽  
Shotgun Metagenomic Sequencing ◽  
Metagenome Assembly ◽  
Environmental Bacteria ◽  
And Function ◽  
Analytical Tools ◽  
Technological Platforms

Shotgun metagenomic sequencing has revolutionized our ability to detect and characterize the diversity and function of complex microbial communities. In this review, we highlight the benefits of using metagenomics as well as the breadth of conclusions that can be made using currently available analytical tools, such as greater resolution of species and strains across phyla and functional content, while highlighting challenges of metagenomic data analysis. Major challenges remain in annotating function, given the dearth of functional databases for environmental bacteria compared to model organisms, and the technical difficulties of metagenome assembly and phasing in heterogeneous environmental samples. In the future, improvements and innovation in technology and methodology will lead to lowered costs. Data integration using multiple technological platforms will lead to a better understanding of how to harness metagenomes. Subsequently, we will be able not only to characterize complex microbiomes but also to manipulate communities to achieve prosperous outcomes for health, agriculture, and environmental sustainability.

scholarly journals Metagenomic Analysis of the Fecal Archaeome in Suckling Piglets Following Perinatal Tulathromycin Metaphylaxis

Animals ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 1825
Author(s):  
Mohamed Zeineldin ◽  
Ameer Megahed ◽  
Benjamin Blair ◽  
Brian Aldridge ◽  
James Lowe
Keyword(s):  
Sequencing Analysis ◽  
Metagenomic Sequencing ◽  
Post Intervention ◽  
Gastrointestinal Microbiome ◽  
Health And Wellbeing ◽  
Suckling Piglets ◽  
And Function ◽  
Changes Over Time ◽  
And Control ◽  
The Impact

The gastrointestinal microbiome plays an important role in swine health and wellbeing, but the gut archaeome structure and function in swine remain largely unexplored. To date, no metagenomics-based analysis has been done to assess the impact of an early life antimicrobials intervention on the gut archaeome. The aim of this study was to investigate the effects of perinatal tulathromycin (TUL) administration on the fecal archaeome composition and diversity in suckling piglets using metagenomic sequencing analysis. Sixteen litters were administered one of two treatments (TUL; 2.5 mg/kg IM and control (CONT); saline 1cc IM) soon after birth. Deep fecal swabs were collected from all piglets on days 0 (prior to treatment), 5, and 20 post intervention. Each piglet’s fecal archaeome was composed of rich and diverse communities that showed significant changes over time during the suckling period. At the phylum level, 98.24% of the fecal archaeome across all samples belonged to Euryarchaeota. At the genus level, the predominant archaeal genera across all samples were Methanobrevibacter (43.31%), Methanosarcina (10.84%), Methanococcus (6.51%), and Methanocorpusculum (6.01%). The composition and diversity of the fecal archaeome between the TUL and CONT groups at the same time points were statistically insignificant. Our findings indicate that perinatal TUL metaphylaxis seems to have a minimal effect on the gut archaeome composition and diversity in sucking piglets. This study improves our current understanding of the fecal archaeome structure in sucking piglets and provides a rationale for future studies to decipher its role in and impact on host robustness during this critical phase of production.

scholarly journals Effects of Dysbiosis and Dietary Manipulation on the Digestive Microbiota of a Detritivorous Arthropod

2021 ◽  
Vol 9 (1) ◽  
pp. 148
Author(s):  
Marius Bredon ◽  
Elisabeth Depuydt ◽  
Lucas Brisson ◽  
Laurent Moulin ◽  
Ciriac Charles ◽  
...  
Keyword(s):  
Crucial Role ◽  
Structure And Function ◽  
Ecological Interactions ◽  
Dietary Manipulation ◽  
Biotic Factors ◽  
Abiotic And Biotic Factors ◽  
And Function ◽  
Multicellular Organisms ◽  
Over Time

The crucial role of microbes in the evolution, development, health, and ecological interactions of multicellular organisms is now widely recognized in the holobiont concept. However, the structure and stability of microbiota are highly dependent on abiotic and biotic factors, especially in the gut, which can be colonized by transient bacteria depending on the host’s diet. We studied these impacts by manipulating the digestive microbiota of the detritivore Armadillidium vulgare and analyzing the consequences on its structure and function. Hosts were exposed to initial starvation and then were fed diets that varied the different components of lignocellulose. A total of 72 digestive microbiota were analyzed according to the type of the diet (standard or enriched in cellulose, lignin, or hemicellulose) and the period following dysbiosis. The results showed that microbiota from the hepatopancreas were very stable and resilient, while the most diverse and labile over time were found in the hindgut. Dysbiosis and selective diets may have affected the host fitness by altering the structure of the microbiota and its predicted functions. Overall, these modifications can therefore have effects not only on the holobiont, but also on the “eco-holobiont” conceptualization of macroorganisms.

scholarly journals Multimorbidity patterns in old adults and their associated multi-layered factors: a cross-sectional study

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
Jiao Lu ◽  
Yuan Wang ◽  
Lihong Hou ◽  
Zhenxing Zuo ◽  
Na Zhang ◽  
...  
Keyword(s):  
Latent Class ◽  
Metabolic Diseases ◽  
Ecological Model ◽  
Explanatory Power ◽  
Cross Sectional Study ◽  
Shanxi Province ◽  
Cluster Sampling ◽  
Cross Sectional ◽  
Old Patients ◽  
Old Adults

Abstract Background Influenced by various factors such as socio-demographic characteristics, behavioral lifestyles and socio-cultural environment, the multimorbidity patterns in old adults remain complex. This study aims to identify their characteristics and associated multi-layered factors based on health ecological model. Methods In 2019, we surveyed a total of 7480 participants aged 60+ by using a multi-stage random cluster sampling method in Shanxi province, China. Latent class analysis was used to discriminate the multimorbidity patterns in old adults, and hierarchical regression was performed to determine the multi-layered factors associated with their various multimorbidity patterns. Results The prevalence of multimorbidity was 34.70% among the old patients with chronic disease. Over half (60.59%) of the patients with multimorbidity had two co-existing chronic diseases. “Degenerative/digestive diseases”, “metabolic diseases” and “cardiovascular diseases” were three specific multimorbidity patterns. Behavioral lifestyles-layered factors had the most explanatory power for the three patterns, whose proportions of explanatory power were 54.00, 43.90 and 48.15% individually. But the contributions of other multi-layered factors were different in different patterns; balanced diet, medication adherence, the size of family and friendship network, and different types of basic medical insurance might have the opposite effect on the three multimorbidity patterns (p < 0.05). Conclusions In management of old patients with multimorbidity, we should prioritize both the “lifestyle change”-centered systematic management strategy and group-customized intervention programs.

scholarly journals Identification of a New Antimicrobial, Desertomycin H, Utilizing a Modified Crowded Plate Technique

Marine Drugs ◽  
2021 ◽  
Vol 19 (8) ◽  
pp. 424
Author(s):  
Osama G. Mohamed ◽  
Sadaf Dorandish ◽  
Rebecca Lindow ◽  
Megan Steltz ◽  
Ifrah Shoukat ◽  
...  
Keyword(s):  
Antibiotic Production ◽  
Gene Clusters ◽  
Multidrug Resistant ◽  
Microbial Interactions ◽  
Mass Spectrometry Data ◽  
Metagenomic Data ◽  
Resistant Bacteria ◽  
Biosynthetic Gene ◽  
Biosynthetic Gene Clusters ◽  
Plate Technique

The antibiotic-resistant bacteria-associated infections are a major global healthcare threat. New classes of antimicrobial compounds are urgently needed as the frequency of infections caused by multidrug-resistant microbes continues to rise. Recent metagenomic data have demonstrated that there is still biosynthetic potential encoded in but transcriptionally silent in cultivatable bacterial genomes. However, the culture conditions required to identify and express silent biosynthetic gene clusters that yield natural products with antimicrobial activity are largely unknown. Here, we describe a new antibiotic discovery scheme, dubbed the modified crowded plate technique (mCPT), that utilizes complex microbial interactions to elicit antimicrobial production from otherwise silent biosynthetic gene clusters. Using the mCPT as part of the antibiotic crowdsourcing educational program Tiny Earth®, we isolated over 1400 antibiotic-producing microbes, including 62, showing activity against multidrug-resistant pathogens. The natural product extracts generated from six microbial isolates showed potent activity against vancomycin-intermediate resistant Staphylococcus aureus. We utilized a targeted approach that coupled mass spectrometry data with bioactivity, yielding a new macrolactone class of metabolite, desertomycin H. In this study, we successfully demonstrate a concept that significantly increased our ability to quickly and efficiently identify microbes capable of the silent antibiotic production.

scholarly journals ENERGY EXPENDITURE AND PHYSICAL ACTIVITY AMONG OLDER PARTICIPANTS FROM THE MULTICENTER AIDS COHORT STUDY (MACS)

2019 ◽  
Vol 3 (Supplement_1) ◽  
pp. S549-S549
Author(s):  
Jennifer A Schrack ◽  
Todd T Brown ◽  
Joseph B Margolick
Keyword(s):  
Physical Activity ◽  
Metabolic Rate ◽  
Resting Metabolic Rate ◽  
Functional Decline ◽  
Time Of Day ◽  
Energy Utilization ◽  
Hiv Viral Load ◽  
Cross Sectional ◽  
And Function ◽  
Lower Physical Activity

Abstract Energy utilization becomes more inefficient with age and is linked to low physical activity and functional decline. Persons aging with HIV exhibit accelerated functional decline, but the effect of chronic HIV infection on energy utilization and free-living physical activity remains unclear. We investigated cross-sectional associations between age and: resting metabolic rate, peak walking energy (VO2), and 7-day physical activity by accelerometry in 100 men in the MACS (age: 60.8+/-6.8 years, 35% black, 46.1% HIV+, 94% virally suppressed). In multivariable regression models adjusted for age, BMI, race, chronic conditions, and HIV viral load, HIV+ men had a higher resting metabolic rate (β=103.2 kcals/day, p=0.03) and lower peak walking VO2 (β=-1.8 ml/kg/min, p&lt;0.02) than HIV- men. Moreover, HIV+ men demonstrated lower physical activity, overall and by time of day (p&lt;0.05). These results suggest that energy utilization differs by HIV serostatus, which may contribute to lower physical activity and function with aging.

The Variable Insertional Anatomy of the Abductor Pollicis Longus: Functional Relevance and Relationship to Adjacent Thumb Extensors

Hand ◽  
2021 ◽  
pp. 155894472199973
Author(s):  
Shruthi Deivasigamani ◽  
Ali Azad ◽  
S. Steven Yang
Keyword(s):  
Cross Sectional Area ◽  
Sectional Area ◽  
Abductor Pollicis Brevis ◽  
Thenar Muscle ◽  
Cross Sectional ◽  
Extensor Pollicis Longus ◽  
Abductor Pollicis Longus ◽  
Branching Patterns ◽  
Functional Relevance ◽  
And Function

Background The abductor pollicis longus (APL) is classically described as inserting on the base of the first metacarpal. This study analyzed APL insertional anatomy and quantified the size of various elements of the extensor side of the thumb to determine associations with size and function. Methods Twenty-four formalin-preserved upper limbs were dissected. The insertional anatomy of the APL, extensor pollicis brevis, and extensor pollicis longus were characterized, and the capacity of APL tendon slips to perform palmar abduction of the first digit was quantified based on slip size and insertion. Results The mean number of APL tendon slips observed was 2.3. Abductor pollicis longus insertion sites included the base of the first metacarpal, trapezium, abductor pollicis brevis, and opponens pollicis. Only 4 specimens had a solitary metacarpal slip, while 83% of specimens had insertions onto at least 1 thenar muscle. A total of 62.5% of APL tendons exhibited some form of branching that we categorized into “Y” and “Z” patterns. In assessing palmar abduction capacity, we found that APL tendon slips inserting into the base of the first metacarpal were larger in cross-sectional area than nonmetacarpal slips and reproduced complete palmar abduction of the digit in the absence of nonmetacarpal slips. The abduction capacity of APL tendon slips was not correlated to the cross-sectional area. Conclusions There is significant variability in APL tendon slips, branching patterns, and insertional anatomy. These findings provide further understanding of the function of the APL and its surgical implications.

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