scholarly journals Diet and Domestication Drive Evolution of the Gut Holobiome

2021 ◽  
Author(s):  
Vivek Ramanan ◽  
Shanti Mechery ◽  
Indra Neil Sarkar
Keyword(s):  
Data Collection ◽  
Microbial Diversity ◽  
Microbial Metabolism ◽  
Wild Relatives ◽  
Microbial Composition ◽  
Fiber Degradation ◽  
Host Diet ◽  
And Behavior ◽  
Host Evolution ◽  
Microbiome Data

The host microbiome encompasses all microorganisms of a host. Host and microbiome coevolution in the gut result in differing microbial compositions, functionality, and host diet [1]. Host diet modulates what macromolecules are used for gut microbial metabolism, which can determine digestion, health, and behavior [2, 3]. Microbial composition across animals provides data on how microbiomes segregate between species and diets [4]. Here we show that microbiome data from GenBank can model host evolution, providing a holobiome insight to the important roles of diet and domestication. The main findings of this study in respect to microbial composition among species were: (1) herbivores are more similar than hosts with other diets; (2) domesticated species are more similar than wild relatives; and (3) humans are distinct from primates. Microbial composition between diets indicates a difference in functionality, where protein and fiber degradation are seen more in carnivores and herbivores respectively. Additionally, herbivores show the most microbial diversity among the diets. Finally, this analysis informs us of gaps in current microbiome data collection, which is biased toward pathogens. Thus, the host-microbiome relationship depicts a complex web of microbial functionality, composition, and diet that impact coevolution.

HONORIFIC CIA-CIA LANGUAGE IN BURU DISTRICT

2020 ◽  
Author(s):  
SUSIATI
Keyword(s):  
Qualitative Research ◽  
Data Collection ◽  
And Behavior

The word 'politeness' can be interpreted as 'politeness'. Although often aligned and paired, polite words and polite words have different meanings. The Big Indonesian Dictionary defines the word polite as respectful and reverent and orderly according to good tradition. Meanwhile, the word courtesy means the subtle and kind nature of his language and behavior. Thus, manners can be interpreted as the nature of respect, orderly to the prevailing norms, smooth and kind language, and good behavior. Therefore, someone who has good manners is someone who is respectful, obedient to the prevailing norms, refined and well-mannered, and has good behavior. This study aims to describe the ambiguity of the Indonesian language used by Cia-cia districk Buru. This type of research is qualitative research that is naturally or in the context of a wholeness. by using descriptive collected in the form of words and not numbers. The data in this study are data that contain ambiguity using the theories of experts when analyzing. Data collection techniques namely after describing the form of words and phrases in Indonesian written by students after that are analyzed according to theory. the results showed that in students' essays there were words and phrases that contained ambiguity.

scholarly journals Microbiota identified from preserved Anopheles

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Bianca E Silva ◽  
Zvifadzo Matsena Zingoni ◽  
Lizette L. Koekemoer ◽  
Yael L. Dahan-Moss
Keyword(s):  
Microbial Diversity ◽  
Vector Competence ◽  
Mosquito Species ◽  
Anopheles Funestus ◽  
Cost Effective ◽  
Diversity Indices ◽  
Malaria Vectors ◽  
Microbial Composition ◽  
Culture Independent ◽  
Culture Dependent

Abstract Background Mosquito species from the Anopheles gambiae complex and the Anopheles funestus group are dominant African malaria vectors. Mosquito microbiota play vital roles in physiology and vector competence. Recent research has focused on investigating the mosquito microbiota, especially in wild populations. Wild mosquitoes are preserved and transported to a laboratory for analyses. Thus far, microbial characterization post-preservation has been investigated in only Aedes vexans and Culex pipiens. Investigating the efficacy of cost-effective preservatives has also been limited to AllProtect reagent, ethanol and nucleic acid preservation buffer. This study characterized the microbiota of African Anopheles vectors: Anopheles arabiensis (member of the An. gambiae complex) and An. funestus (member of the An. funestus group), preserved on silica desiccant and RNAlater® solution. Methods Microbial composition and diversity were characterized using culture-dependent (midgut dissections, culturomics, MALDI-TOF MS) and culture-independent techniques (abdominal dissections, DNA extraction, next-generation sequencing) from laboratory (colonized) and field-collected mosquitoes. Colonized mosquitoes were either fresh (non-preserved) or preserved for 4 and 12 weeks on silica or in RNAlater®. Microbiota were also characterized from field-collected An. arabiensis preserved on silica for 8, 12 and 16 weeks. Results Elizabethkingia anophelis and Serratia oryzae were common between both vector species, while Enterobacter cloacae and Staphylococcus epidermidis were specific to females and males, respectively. Microbial diversity was not influenced by sex, condition (fresh or preserved), preservative, or preservation time-period; however, the type of bacterial identification technique affected all microbial diversity indices. Conclusions This study broadly characterized the microbiota of An. arabiensis and An. funestus. Silica- and RNAlater®-preservation were appropriate when paired with culture-dependent and culture-independent techniques, respectively. These results broaden the selection of cost-effective methods available for handling vector samples for downstream microbial analyses.

Risk perception and awareness of earthquake: the case of Dhaka

2019 ◽  
Vol 10 (1) ◽  
pp. 65-82 ◽  
Author(s):  
Mohammad Lutfur Rahman
Keyword(s):  
Risk Perception ◽  
Data Collection ◽  
Seismic Risk ◽  
Public Awareness ◽  
Content Type ◽  
Earthquake Preparedness ◽  
Level Of Knowledge ◽  
Seismic Risk Perception ◽  
The Many ◽  
And Behavior

Purpose Among the many studies about risk perception, only a few deal with Bangladesh. Paul and Bhuiyan’s (2010) study has shown the earthquake-preparedness level of residents of Dhaka, but there are some biases in the data collection. This paper aims to examine the seismic-risk perception and the level of knowledge on earthquake and preparedness among the residents of Dhaka. Design/methodology/approach A questionnaire was developed, and data collection was undertaken through home and sidewalk surveys. This paper investigates how attitude, perception and behavior differ depending on gender, age, education and casualty awareness. This research tries to examine and make a comparison of the risk perception and preparedness level between different groups of gender, age and level of education. Findings This research shows that female respondents have a much better risk perception of and are better prepared for earthquakes than male respondents; younger people have a higher knowledge about earthquake preparedness than older people and less-educated people are at a higher risk of unpreparedness than more-educated people. Research limitations/implications This research is only limited to the Dhaka Division. Originality/value This paper concludes by noting that public awareness on seismic-risk perception and mitigation is poor, and their knowledge on basic theory and emergency response must be improved.

scholarly journals Longitudinal sampling of external mucosae in farmed European seabass reveals the impact of water temperature on bacterial dynamics

2021 ◽  
Vol 1 (1) ◽  
Author(s):  
Daniela Rosado ◽  
Raquel Xavier ◽  
Jo Cable ◽  
Ricardo Severino ◽  
Pedro Tarroso ◽  
...  
Keyword(s):  
Environmental Factors ◽  
Microbial Diversity ◽  
Water Temperature ◽  
Abiotic Factors ◽  
Seasonal Effect ◽  
Microbial Composition ◽  
Surrounding Water ◽  
European Seabass ◽  
And Function ◽  
The Impact

AbstractFish microbiota are intrinsically linked to health and fitness, but they are highly variable and influenced by both biotic and abiotic factors. Water temperature particularly limits bacterial adhesion and growth, impacting microbial diversity and bacterial infections on the skin and gills. Aquaculture is heavily affected by infectious diseases, especially in warmer months, and industry practices often promote stress and microbial dysbiosis, leading to an increased abundance of potentially pathogenic bacteria. In this regard, fish mucosa health is extremely important because it provides a primary barrier against pathogens. We used 16 rRNA V4 metataxonomics to characterize the skin and gill microbiota of the European seabass, Dicentrarchus labrax, and the surrounding water over 12 months, assessing the impact of water temperature on microbial diversity and function. We show that the microbiota of external mucosae are highly dynamic with consistent longitudinal trends in taxon diversity. Several potentially pathogenic genera (Aliivibrio, Photobacterium, Pseudomonas, and Vibrio) were highly abundant, showing complex interactions with other bacterial genera, some of which with recognized probiotic activity, and were also significantly impacted by changes in temperature. The surrounding water temperature influenced fish microbial composition, structure and function over time (days and months). Additionally, dysbiosis was more frequent in warmer months and during transitions between cold/warm months. We also detected a strong seasonal effect in the fish microbiota, which is likely to result from the compound action of several unmeasured environmental factors (e.g., pH, nutrient availability) beyond temperature. Our results highlight the importance of performing longitudinal studies to assess the impact of environmental factors on fish microbiotas.

scholarly journals Bioconductor workflow for microbiome data analysis: from raw reads to community analyses

F1000Research ◽  
2016 ◽  
Vol 5 ◽  
pp. 1492 ◽  
Author(s):  
Ben J. Callahan ◽  
Kris Sankaran ◽  
Julia A. Fukuyama ◽  
Paul J. McMurdie ◽  
Susan P. Holmes
Keyword(s):  
High Throughput Sequencing ◽  
Linear Models ◽  
Reference Database ◽  
Rrna Gene ◽  
Microbial Composition ◽  
Nonparametric Testing ◽  
Abundance Estimates ◽  
Taxonomic Markers ◽  
Microbiome Data ◽  
Microbiome Data Analysis

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or microbial composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, including both parameteric and nonparametric methods. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests, partial least squares and linear models as well as nonparametric testing using community networks and the ggnetwork package.

scholarly journals The Effect of Light Intensity, Strain, and Age on the Behavior, Jumping Frequency and Success, and Welfare of Egg-Strain Pullets Reared in Perchery Systems

Animals ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 3353
Author(s):  
Jo Ann Chew ◽  
Tina Widowski ◽  
Eugenia Herwig ◽  
Tory Shynkaruk ◽  
Karen Schwean-Lardner
Keyword(s):  
Data Collection ◽  
Light Intensity ◽  
Novel Object ◽  
Continuous Sampling ◽  
And Behavior ◽  
Effect Of Light

The effects of light intensity (L) are not well studied in pullets. Our research objective was to study the effect of L on navigational success, behavior, and welfare of two pullet strains (S). In two repeated trials, a 3 × 2 × 4 factorial arrangement tested three L (10, 30, 50 lux) and two S (Lohmann Brown-Lite (LB), LSL-Lite (LW)) at four ages. One thousand eight hundred pullets/S (0–16 wk) were randomly assigned to floor pens within light-tight rooms (three pens/S/room, four rooms/L) containing four parallel perches and a ramp. Data collection included jumping frequency and success (24h continuous sampling), novel object tests (fear), heterophil to lymphocyte (H/L) ratios (stress), and behavior (instantaneous scan sampling) during photoperiods. L did not affect injurious behavior, fear, or H/L. Pullets reared at 50 lux spent more time preening than at 10 lux. Pullets reared at 10 lux spent more time wall pecking than at 50 lux. Time spent standing and preening and total number and accuracy of jumping increased with age. Pullets reared at 30 lux had higher jumping frequency than at 10 lux; accuracy was not affected. LW jumped more than LB, but with similar success. LB spent more time exploring and scored higher in the fear and stress assessments, suggesting S differences.

scholarly journals A joint modeling approach for longitudinal microbiome data improves ability to detect microbiome associations with disease

2020 ◽  
Vol 16 (12) ◽  
pp. e1008473
Author(s):  
Pamela N. Luna ◽  
Jonathan M. Mansbach ◽  
Chad A. Shaw
Keyword(s):  
Joint Modeling ◽  
Mixed Effects ◽  
Mixed Effects Model ◽  
Time Dependent ◽  
Time To Event ◽  
Modeling Framework ◽  
Microbial Composition ◽  
Disease Outcomes ◽  
Microbiome Data ◽  
Over Time

Changes in the composition of the microbiome over time are associated with myriad human illnesses. Unfortunately, the lack of analytic techniques has hindered researchers’ ability to quantify the association between longitudinal microbial composition and time-to-event outcomes. Prior methodological work developed the joint model for longitudinal and time-to-event data to incorporate time-dependent biomarker covariates into the hazard regression approach to disease outcomes. The original implementation of this joint modeling approach employed a linear mixed effects model to represent the time-dependent covariates. However, when the distribution of the time-dependent covariate is non-Gaussian, as is the case with microbial abundances, researchers require different statistical methodology. We present a joint modeling framework that uses a negative binomial mixed effects model to determine longitudinal taxon abundances. We incorporate these modeled microbial abundances into a hazard function with a parameterization that not only accounts for the proportional nature of microbiome data, but also generates biologically interpretable results. Herein we demonstrate the performance improvements of our approach over existing alternatives via simulation as well as a previously published longitudinal dataset studying the microbiome during pregnancy. The results demonstrate that our joint modeling framework for longitudinal microbiome count data provides a powerful methodology to uncover associations between changes in microbial abundances over time and the onset of disease. This method offers the potential to equip researchers with a deeper understanding of the associations between longitudinal microbial composition changes and disease outcomes. This new approach could potentially lead to new diagnostic biomarkers or inform clinical interventions to help prevent or treat disease.

scholarly journals Implementasi Reward dan Punishment Dalam Membentuk Karakter Disiplin Peserta Didik Di Madrasah Ibtidaiyah Al-Hidayah Jember

2021 ◽  
Vol 2 (1) ◽  
pp. 87-100
Author(s):  
Siti Nur Fadilah ◽  
Nasirudin F
Keyword(s):  
Data Collection ◽  
Character Education ◽  
Process Evaluation ◽  
Learning Process ◽  
Qualitative Approach ◽  
Study Methods ◽  
And Behavior ◽  
Case Study Methods ◽  
The Way

Giving stimulus from educators in the form of giving appreciation and punishment will greatly affect the way of thinking and behavior of students in achieving the goals of character education that have been set. This study aims to describe the implementation of reward and punishment in shaping the character of students' discipline. This research uses a qualitative approach with the type of case study. Methods of data collection using interviews, observation and documentation. The validity of the data used source triangulation and technical triangulation. The results of this study indicate: (1) The implementation of rewards in shaping the discipline character of students is done by giving rewards in the form of praise and giving appreciation in the form of gifts. (2) The implementation of punishment in shaping the disciplinary character of students is carried out by giving gradual warnings, giving spontaneous warnings and written warning letters. (3) Evaluation of the implementation of rewards and punishments in shaping the character of students' discipline is using process evaluation, which is an assessment carried out during the learning process by observing the attitudes of students everyday when they are in the madrasa environment.. Keywords: Reward; Punishment; Discipline; Learners Pemberian stimulus dari pendidik berupa pemberian apresiasi dan hukuman akan sangat mempengaruhi cara berpikir dan tingkah laku peserta didik dalam mencapai tujuan pendidikan karakter yang sudah ditetapkan. Penelitian ini bertujuan untuk mendeskripsikan implementasi reward dan punishment dalam membentuk karakter disiplin peserta didik. Penelitian ini menggunakan pendekatan kualitatif dengan jenis studi kasus. Metode pengumpulan data menggunakan wawancara, observasi dan dokumentasi. Keabsahan data menggunakan triangulasi sumber dan triangulasi tehnik. Hasil penelitian ini menunjukkan: (1) Implementasi reward dalam membentuk karakter kedisiplinan peserta didik dilakukan dengan memberikan reward dalam bentuk pujian serta memberikan apresiasi dalam bentuk hadiah. (2) Implementasi punishment dalam membentuk karakter kedisiplinan peserta didik dilakukan dengan cara memberi peringatan secara bertahap, memberi teguran spontan dan surat peringatan tertulis. (3) Evaluasi implementasi reward dan punishment dalam membentuk karakter kedisiplinan peserta didik adalah menggunakan evaluasi proses, yaitu penilaian yang dilakukan di saat proses pembelajaran berlangsung dengan mengamati dari sikap peserta didik sehari-hari ketika berada di lingkungan madrasah. Kata Kunci: Reward; Punishment; Disiplin; Peserta Didik

scholarly journals Persistence of the ground beetle (Coleoptera: Carabidae) microbiome to diet manipulation

PLoS ONE ◽  
2021 ◽  
Vol 16 (3) ◽  
pp. e0241529
Author(s):  
Anita Silver ◽  
Sean Perez ◽  
Melanie Gee ◽  
Bethany Xu ◽  
Shreeya Garg ◽  
...  
Keyword(s):  
Microbial Diversity ◽  
Ground Beetle ◽  
Amplicon Sequencing ◽  
Carabid Beetles ◽  
Secretory Cells ◽  
Pygidial Gland ◽  
Defensive Compounds ◽  
Highly Active ◽  
16S Amplicon Sequencing ◽  
Host Diet

Host-associated microbiomes can play important roles in the ecology and evolution of their insect hosts, but bacterial diversity in many insect groups remains poorly understood. Here we examine the relationship between host environment, host traits, and microbial diversity in three species in the ground beetle family (Coleoptera: Carabidae), a group of roughly 40,000 species that synthesize a wide diversity of defensive compounds. This study used 16S amplicon sequencing to profile three species that are phylogenetically distantly related, trophically distinct, and whose defensive chemical secretions differ: Anisodactylus similis LeConte, 1851, Pterostichus serripes (LeConte, 1875), and Brachinus elongatulus Chaudoir, 1876. Wild-caught beetles were compared to individuals maintained in the lab for two weeks on carnivorous, herbivorous, or starvation diets (n = 3 beetles for each species-diet combination). Metagenomic samples from two highly active tissue types—guts, and pygidial gland secretory cells (which produce defensive compounds)—were processed and sequenced separately from those of the remaining body. Bacterial composition and diversity of these ground beetles were largely resilient to controlled changes to host diet. Different tissues within the same beetle harbor unique microbial communities, and secretory cells in particular were remarkably similar across species. We also found that these three carabid species have patterns of microbial diversity similar to those previously found in carabid beetles. These results provide a baseline for future studies of the role of microbes in the diversification of carabids.

Sign in / Sign up

Export Citation Format

Share Document