scholarly journals Detection of stable community structures within gut microbiota co-occurrence networks from different human populations

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4303 ◽  
Author(s):  
Matthew A. Jackson ◽  
Marc Jan Bonder ◽  
Zhana Kuncheva ◽  
Jonas Zierer ◽  
Jingyuan Fu ◽  
...  
Keyword(s):  
Community Structure ◽  
Gut Microbiota ◽  
Human Populations ◽  
Specific Interactions ◽  
Diverse Populations ◽  
Community Structures ◽  
Operational Taxonomic Units ◽  
Novel Approach ◽  
Different Populations ◽  
Multiple Samples

Microbes in the gut microbiome form sub-communities based on shared niche specialisations and specific interactions between individual taxa. The inter-microbial relationships that define these communities can be inferred from the co-occurrence of taxa across multiple samples. Here, we present an approach to identify comparable communities within different gut microbiota co-occurrence networks, and demonstrate its use by comparing the gut microbiota community structures of three geographically diverse populations. We combine gut microbiota profiles from 2,764 British, 1,023 Dutch, and 639 Israeli individuals, derive co-occurrence networks between their operational taxonomic units, and detect comparable communities within them. Comparing populations we find that community structure is significantly more similar between datasets than expected by chance. Mapping communities across the datasets, we also show that communities can have similar associations to host phenotypes in different populations. This study shows that the community structure within the gut microbiota is stable across populations, and describes a novel approach that facilitates comparative community-centric microbiome analyses.

scholarly journals Codiversification of gut microbiota with humans

2021 ◽  
Author(s):  
Taichi A. Suzuki ◽  
Liam Fitzstevens ◽  
Victor T. Schmidt ◽  
Hagay Enav ◽  
Kelsey Huus ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Vertical Transmission ◽  
Evolutionary History ◽  
Human Populations ◽  
African Origin ◽  
Strain Transfer ◽  
Close Proximity ◽  
Different Populations ◽  
Specific Health

Some gut microbes have cospeciated with hominids, but whether they further codiversified with human populations is unclear. Here, we identify predominant gut microbial species sharing a parallel evolutionary history with human populations. Patterns of strain transfer between populations are generally consistent with an African origin, and suggest long-term vertical transmission over thousands of generations. We show the same strains also faithfully transmit between mothers and their children. Consistent with the development of intimate symbiosis, species with strongest patterns of codiversification have the smallest genomes. This study reveals long-term fidelity of gut microbiota with human populations through transmission among individuals living in close proximity. Dominance of specific strains in different populations is based in part on vertical transmission and they may provide population-specific health benefits.

scholarly journals Tracking human population structure through time from whole genome sequences

2019 ◽  
Author(s):  
Ke Wang ◽  
Iain Mathieson ◽  
Jared O’Connell ◽  
Stephan Schiffels
Keyword(s):  
Population Structure ◽  
Gene Flow ◽  
Demographic History ◽  
Time Dependent ◽  
Human Populations ◽  
Whole Genome ◽  
Genome Sequences ◽  
Migration Model ◽  
Novel Approach ◽  
Different Populations

AbstractThe genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population’s history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyse the population separation history. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.Author SummaryHuman demographic history is reflected in specific patterns of shared mutations between the genomes from different populations. Here we aim to unravel this pattern to infer population structure through time with a new approach, called MSMC-IM. Based on estimates of coalescence rates within and across populations, MSMC-IM fits a time-dependent migration model to the pairwise rate of coalescences. We implemented this approach as an extension to existing software (MSMC2), and tested it with simulations exhibiting different histories of admixture and gene flow. We then applied it to the genomes from 15 worldwide populations to reveal their pairwise separation history ranging from a few thousand up to several million years ago. Among other results, we find evidence for remarkably deep population structure in some African population pairs, suggesting that deep ancestry dating to one million years ago and older is still present in human populations in small amounts today.

scholarly journals Comparative Analysis of Fecal Microbiota of Grazing Mongolian Cattle from Different Regions in Inner Mongolia, China

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1938
Author(s):  
Han Aricha ◽  
Huasai Simujide ◽  
Chunjie Wang ◽  
Jian Zhang ◽  
Wenting Lv ◽  
...  
Keyword(s):  
Community Structure ◽  
Microbial Community ◽  
Gut Microbiota ◽  
Inner Mongolia ◽  
Alpha Diversity ◽  
Fecal Microbiota ◽  
Composition Analysis ◽  
Geographical Factors ◽  
Rrna Sequencing ◽  
Xilingol Grassland

Mongolian cattle from China have strong adaptability and disease resistance. We aimed to compare the gut microbiota community structure and diversity in grazing Mongolian cattle from different regions in Inner Mongolia and to elucidate the influence of geographical factors on the intestinal microbial community structure. We used high throughput 16S rRNA sequencing to analyze the fecal microbial community and diversity in samples from 60 grazing Mongolian cattle from Hulunbuir Grassland, Xilingol Grassland, and Alxa Desert. A total of 2,720,545 high-quality reads and sequences that were 1,117,505,301 bp long were obtained. Alpha diversity among the three groups showed that the gut microbial diversity in Mongolian cattle in the grasslands was significantly higher than that in the desert. The dominant phyla were Firmicutes and Bacteroidetes, whereas Verrucomicrobia presented the highest abundance in the gut of cattle in the Alxa Desert. The gut bacterial communities in cattle from the grasslands versus the Alxa Desert were distinctive, and those from the grasslands were closely clustered. Community composition analysis revealed significant differences in species diversity and richness. Overall, the composition of the gut microbiota in Mongolian cattle is affected by geographical factors. Gut microbiota may play important roles in the geographical adaptations of Mongolian cattle.

scholarly journals 3D Insights into the Effects of Captivity on Wolf Mastication and Their Tooth Marks; Implications in Ecological Studies of Both the Past and Present

Animals ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 2323
Author(s):  
Lloyd A. Courtenay ◽  
Darío Herranz-Rodrigo ◽  
José Yravedra ◽  
José Mª Vázquez-Rodríguez ◽  
Rosa Huguet ◽  
...  
Keyword(s):  
Data Science ◽  
Surface Modifications ◽  
Human Populations ◽  
Ecological Studies ◽  
The Past ◽  
Carnivore Species ◽  
Different Populations ◽  
Complex Relationships ◽  
As Stress ◽  
Tooth Marks

Human populations have been known to develop complex relationships with large carnivore species throughout time, with evidence of both competition and collaboration to obtain resources throughout the Pleistocene. From this perspective, many archaeological and palaeontological sites present evidence of carnivore modifications to bone. In response to this, specialists in the study of microscopic bone surface modifications have resorted to the use of 3D modeling and data science techniques for the inspection of these elements, reaching novel limits for the discerning of carnivore agencies. The present research analyzes the tooth mark variability produced by multiple Iberian wolf individuals, with the aim of studying how captivity may affect the nature of tooth marks left on bone. In addition to this, four different populations of both wild and captive Iberian wolves are also compared for a more in-depth comparison of intra-species variability. This research statistically shows that large canid tooth pits are the least affected by captivity, while tooth scores appear more superficial when produced by captive wolves. The superficial nature of captive wolf tooth scores is additionally seen to correlate with other metric features, thus influencing overall mark morphologies. In light of this, the present study opens a new dialogue on the reasons behind this, advising caution when using tooth scores for carnivore identification and contemplating how elements such as stress may be affecting the wolves under study.

Urban community structure detection based on the OD of traffic analysis zones

2019 ◽  
Vol 33 (13) ◽  
pp. 1950164
Author(s):  
Qing-Feng Dong ◽  
Dian-Kun Chen ◽  
Ting Wang
Keyword(s):  
Community Structure ◽  
Quantitative Methods ◽  
Urban Community ◽  
Spatial Location ◽  
Traffic Analysis ◽  
Association Mining ◽  
Community Structures ◽  
City Community ◽  
Traffic Characteristics ◽  
Structure Detection

At present, the detection of urban community structures is mainly based on existing administrative divisions, and is performed using qualitative methods. The lack of quantitative methods makes it difficult to judge the rationality of urban community divisions. In this study, we used complex network association mining methods to detect a city community structure by using the Origin-Destinations (OD) at traffic analysis zone (TAZ) level, and successively assigned all the TAZs into different communities. Based on the community results, we calculated the community core degree of each TAZ within every community, and then calculated the Traffic Core Degree and Location Core Degree indicators of the community based on OD passenger flow and spatial location relationship between communities. Finally, we analyzed the correlation among three indicators to ensure the rationality of the community structure. We used the city of Zhengzhou in 2016 as an example case study. For Zhengzhou, we detected a total of six communities. We found a relatively low correlation between Traffic Core Degree and Location Core Degree. Within each group, the correlation between community core degree and Traffic Core Degree was higher than that between community core degree and Location Core Degree, indicating that the urban community structure is more reasonably based on traffic characteristics. The development of a quantitative approach for determining reasonable city community structures has important implications for transportation planning and industrial layout.

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