scholarly journals A simple microbiome in the European common cuttlefish, Sepia officinalis

2018 ◽  
Author(s):  
Holly L. Lutz ◽  
S. Tabita Ramírez-Puebla ◽  
Lisa Abbo ◽  
Amber Durand ◽  
Cathleen Schlundt ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Amplicon Sequencing ◽  
Sepia Officinalis ◽  
16S Rrna Amplicon Sequencing ◽  
The Family ◽  
In Captivity ◽  
Aliivibrio Fischeri ◽  
Small Clusters ◽  
Discrete Layer

ABSTRACTThe European common cuttlefish, Sepia officinalis, is used extensively in biological and biomedical research yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raised S. officinalis using a combination of 16S rRNA amplicon sequencing, qPCR and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) of Vibrionaceae and Piscirickettsiaceae. The esophagus was dominated by a single ASV of the genus Vibrio. Imaging revealed bacteria in the family Vibrionaceae distributed in a discrete layer that lines the esophagus. This Vibrio was also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance as determined by qPCR and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly-used antibiotic enrofloxacin led to a nearly 80% reduction of the dominant Vibrio ASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills was dominated by a single ASV in the family Piscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to the Gammaproteobacteria are the major symbionts of the cuttlefish Sepia officinalis cultured from eggs in captivity, and that the esophagus and gills are major colonization sites.IMPORTANCEMicrobes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role of Vibrio (Aliivibrio) fischeri in the light organ of the bobtail squid and the role of Alpha- and Gammaproteobacteria in the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genus Vibrio, as well as colonization of gills by Piscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated with Vibrio and is of potential significance for understanding host-symbiont associations as well as for understanding and maintaining the health of cephalopods in mariculture.

scholarly journals A Simple Microbiome in the European Common Cuttlefish,Sepia officinalis

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Holly L. Lutz ◽  
S. Tabita Ramírez-Puebla ◽  
Lisa Abbo ◽  
Amber Durand ◽  
Cathleen Schlundt ◽  
...  
Keyword(s):  
Digestive Tract ◽  
Amplicon Sequencing ◽  
Sepia Officinalis ◽  
Content Type ◽  
16S Rrna Amplicon Sequencing ◽  
The Family ◽  
In Captivity ◽  
Small Clusters ◽  
Discrete Layer

ABSTRACTThe European common cuttlefish,Sepia officinalis, is used extensively in biological and biomedical research, yet its microbiome remains poorly characterized. We analyzed the microbiota of the digestive tract, gills, and skin in mariculture-raisedS. officinalisusing a combination of 16S rRNA amplicon sequencing, quantitative PCR (qPCR), and fluorescence spectral imaging. Sequencing revealed a highly simplified microbiota consisting largely of two single bacterial amplicon sequence variants (ASVs) ofVibrionaceaeandPiscirickettsiaceae. The esophagus was dominated by a single ASV of the genusVibrio. Imaging revealed bacteria in the familyVibrionaceaedistributed in a discrete layer that lines the esophagus. ThisVibriowas also the primary ASV found in the microbiota of the stomach, cecum, and intestine, but occurred at lower abundance, as determined by qPCR, and was found only scattered in the lumen rather than in a discrete layer via imaging analysis. Treatment of animals with the commonly used antibiotic enrofloxacin led to a nearly 80% reduction of the dominantVibrioASV in the esophagus but did not significantly alter the relative abundance of bacteria overall between treated versus control animals. Data from the gills were dominated by a single ASV in the familyPiscirickettsiaceae, which imaging visualized as small clusters of cells. We conclude that bacteria belonging to theGammaproteobacteriaare the major symbionts of the cuttlefishSepia officinaliscultured from eggs in captivity and that the esophagus and gills are major colonization sites.IMPORTANCEMicrobes can play critical roles in the physiology of their animal hosts, as evidenced in cephalopods by the role ofVibrio(Aliivibrio)fischeriin the light organ of the bobtail squid and the role ofAlpha- andGammaproteobacteriain the reproductive system and egg defense in a variety of cephalopods. We sampled the cuttlefish microbiome throughout the digestive tract, gills, and skin and found dense colonization of an unexpected site, the esophagus, by a microbe of the genusVibrio, as well as colonization of gills byPiscirickettsiaceae. This finding expands the range of organisms and body sites known to be associated withVibrioand is of potential significance for understanding host-symbiont associations, as well as for understanding and maintaining the health of cephalopods in mariculture.

scholarly journals Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

2020 ◽  
Author(s):  
Kasun H Bodawatta ◽  
Katerina Puzejova ◽  
Katerina Sam ◽  
Michael Poulsen ◽  
Knud A. Jønsson
Keyword(s):  
Microbial Communities ◽  
Digestive Tract ◽  
Wild Bird ◽  
Anthropogenic Impacts ◽  
Parus Major ◽  
Amplicon Sequencing ◽  
Cloacal Swab ◽  
Non Invasive ◽  
16S Rrna Amplicon Sequencing ◽  
Microbiome Research

Abstract Background Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these community-level differences, swab samples qualitatively captured the majority of the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions Our findings suggest that cloacal swabs, similar to non-invasive fecal sampling, qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco Enrique Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian Angelica Bernal Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

scholarly journals Localization of bacterial communities within gut compartments across Cephalotes turtle ants

2021 ◽  
Author(s):  
Peter J. Flynn ◽  
Catherine L. D’Amelio ◽  
Jon G. Sanders ◽  
Jacob A. Russell ◽  
Corrie S. Moreau
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Digestive Tract ◽  
Bacterial Communities ◽  
Evolutionary History ◽  
Amplicon Sequencing ◽  
Caste Differentiation ◽  
Animal Group ◽  
16S Rrna Amplicon Sequencing ◽  
Host Phylogeny

Microbial communities within the animal digestive tract often provide important functions for their hosts. The composition of eukaryotes' gut bacteria can be shaped by host diet, vertical bacterial transmission, and physiological variation within the digestive tract. In several ant taxa, recent findings have demonstrated that nitrogen provisioning by symbiotic bacteria makes up for deficiencies in herbivorous diets. Using 16S rRNA amplicon sequencing and qPCR, this study examined bacterial communities at a fine scale across one such animal group, the turtle ant genus Cephalotes. We analyzed the composition and colonization density across four portions of the digestive tract to understand how bacterial diversity is structured across gut compartments, potentially allowing for specific metabolic functions of benefit to the host. In addition, we aimed to understand if caste differentiation or host relatedness influences the gut bacterial communities of Cephalotes ants. Microbial communities were found to vary strongly across Cephalotes gut compartments in ways that transcend both caste and host phylogeny. Despite this, caste and host phylogeny still have detectable effects. We demonstrated microbial community divergence across gut compartments, possibly due to the varying function of each gut compartment for digestion. IMPORTANCE Gut compartments play an important role in structuring the microbial community within individual ants. The gut chambers of the turtle ant digestive tract differ remarkably in symbiont abundance and diversity. Furthermore, caste type explains some variation in the microbiome composition. Finally, the evolutionary history of the Cephalotes species structures the microbiome in our study, which elucidates a trend in which related ants maintain related microbiomes, conceivably owing to co-speciation. Amazingly, gut compartment-specific signatures of microbial diversity, relative abundance, composition, and abundance have been conserved over Cephalotes evolutionary history, signifying that this symbiosis has been largely stable for over 50 million years.

scholarly journals Acetotrophic Activity Facilitates Methanogenesis from LCFA at Low Temperatures: Screening from Mesophilic Inocula

Archaea ◽  
2019 ◽  
Vol 2019 ◽  
pp. 1-16 ◽  
Author(s):  
Suniti Singh ◽  
Johanna M. Rinta-Kanto ◽  
Riitta Kettunen ◽  
Piet Lens ◽  
Gavin Collins ◽  
...  
Keyword(s):  
Methane Production ◽  
Low Temperatures ◽  
Granular Sludge ◽  
Amplicon Sequencing ◽  
Anaerobic Treatment ◽  
Dairy Wastewater ◽  
Anaerobic Microorganisms ◽  
The Family ◽  
Thermophilic Conditions

The inoculum source plays a crucial role in the anaerobic treatment of wastewaters. Lipids are present in various wastewaters and have a high methanogenic potential, but their hydrolysis results in the production of long chain fatty acids (LCFAs) that are inhibitory to anaerobic microorganisms. Screening of inoculum for the anaerobic treatment of LCFA-containing wastewaters has been performed at mesophilic and thermophilic conditions. However, an evaluation of inocula for producing methane from LCFA-containing wastewater has not yet been conducted at low temperatures and needs to be undertaken. In this study, three inocula (one granular sludge and two municipal digester sludges) were assessed for methane production from LCFA-containing synthetic dairy wastewater (SDW) at low temperatures (10 and 20°C). A methane yield (based on mL-CH4/g-CODadded) of 86-65% with acetate and 45-20% with SDW was achieved within 10 days using unacclimated granular sludge, whereas the municipal digester sludges produced methane only at 20°C but not at 10°C even after 200 days of incubation. The acetotrophic activity in the inoculum was found to be crucial for methane production from LCFA at low temperatures, highlighting the role ofMethanosaeta(acetoclastic archaea) at low temperatures. The presence of bacterial taxa from the familySyntrophaceae(Syntrophusand uncultured taxa) in the inoculum was found to be important for methane production from SDW at 10°C. This study suggests the evaluation of acetotrophic activity and the initial microbial community characteristics by high-throughput amplicon sequencing for selecting the inoculum for producing methane at low temperatures (up to 10°C) from lipid-containing wastewaters.

scholarly journals Low bacterial community diversity in two introduced aphid pests revealed with 16S rRNA amplicon sequencing

PeerJ ◽  
2018 ◽  
Vol 6 ◽  
pp. e4725 ◽  
Author(s):  
Francisca Zepeda-Paulo ◽  
Sebastían Ortiz-Martínez ◽  
Andrea X. Silva ◽  
Blas Lavandero
Keyword(s):  
Bacterial Community ◽  
16S Rrna ◽  
Amplicon Sequencing ◽  
Aphid Species ◽  
Community Diversity ◽  
Cereal Aphids ◽  
Bacterial Community Diversity ◽  
16S Rrna Amplicon Sequencing ◽  
Secondary Endosymbiont

Bacterial endosymbionts that produce important phenotypic effects on their hosts are common among plant sap-sucking insects. Aphids have become a model system of insect-symbiont interactions. However, endosymbiont research has focused on a few aphid species, making it necessary to make greater efforts to other aphid species through different regions, in order to have a better understanding of the role of endosymbionts in aphids as a group. Aphid endosymbionts have frequently been studied by PCR-based techniques, using species-specific primers, nevertheless this approach may omit other non-target bacteria cohabiting a particular host species. Advances in high-throughput sequencing technologies are complementing our knowledge of microbial communities by allowing us the study of whole microbiome of different organisms. We used a 16S rRNA amplicon sequencing approach to study the microbiome of aphids in order to describe the bacterial community diversity in introduced populations of the cereal aphids, Sitobion avenae and Rhopalosiphum padi in Chile (South America). An absence of secondary endosymbionts and two common secondary endosymbionts of aphids were found in the aphids R. padi and S. avenae, respectively. Of those endosymbionts, Regiella insecticola was the dominant secondary endosymbiont among the aphid samples. In addition, the presence of a previously unidentified bacterial species closely related to a phytopathogenic Pseudomonad species was detected. We discuss these results in relation to the bacterial endosymbiont diversity found in other regions of the native and introduced range of S. avenae and R. padi. A similar endosymbiont diversity has been reported for both aphid species in their native range. However, variation in the secondary endosymbiont infection could be observed among the introduced and native populations of the aphid S. avenae, indicating that aphid-endosymbiont associations can vary across the geographic range of an aphid species. In addition, we discuss the potential role of aphids as vectors and/or alternative hosts of phytopathogenic bacteria.

scholarly journals 16S rRNA Amplicon Sequencing of Bagworm Metisa plana Walker (Lepidoptera: Psychidae)

2021 ◽  
Author(s):  
Andrew Chung Jie Ting ◽  
Cik Mohd Rizuan ZAINAL ABIDIN ◽  
Noor Hisham HAMID ◽  
Ghows Azzam ◽  
Hasber Salim
Keyword(s):  
Community Structure ◽  
Bacterial Community ◽  
Bacterial Community Structure ◽  
Amplicon Sequencing ◽  
16S Rrna Amplicon Sequencing ◽  
Outbreak Area ◽  
The Family ◽  
Family Level ◽  
Late Instar ◽  
Early Instar

The bagworm Metisa plana is one of the major pests in the oil palm plantation in Malaysia, with infestation that results in huge economical loss. Currently, the exact cause of the infestation is still undetermined. Studying the bacterial community of M. plana could provide insight on the problem as the bacteria associated with insects often provide numerous benefits to the insect itself. Using 16S rRNA amplicon sequencing, the study was conducted to compare the composition of the bacterial communities of two larval stages (early instar stage and late instar stage) from outbreak area, as well as comparing the late instar stage larvae from non-outbreak and outbreak areas. Generally, the bacterial community was dominated by Proteobacteria and Actinobacteria phyla while the Enterobacteriaceae was found to be the dominant family. When comparing between the early and late instar stage, Proteobacteria phylum was found to be more abundant in the late instar stage (82.36%) than in the early instar stage (82.28%). At the family level, the Enterobacteriaceae was slightly more abundant in late instar stage (75.46%) than in early instar stage (75.29%). The instar stage was observed to have no significant impact on the bacterial variability and showed similar bacterial community structure. When comparing between the non-outbreak area and outbreak, Proteobacteria was significantly more abundant in the outbreak area (82.02%) than in the non-outbreak area (20.57%). However, Actinobacteria was significantly more abundant in the non-outbreak area (76.29%) than in the outbreak area (14.16%). At the family level, Enterobacteriaceae was more abundant in outbreak area (75.41%) than in non-outbreak area (11.67%). Microbacteriaceae was observed to be more abundant in the non-outbreak area (70.87%) than in the outbreak area (12.47%). Although the result showed no significant difference in bacterial variability between different areas, it the bacterial community structure was significantly different.

scholarly journals Experimental evidence pointing to rain as a reservoir of tomato phyllosphere microbiota

2021 ◽  
Author(s):  
Marco E Mechan Llontop ◽  
Long Tian ◽  
Parul Sharma ◽  
Logan Heflin ◽  
Vivian A Bernal-Galeano ◽  
...  
Keyword(s):  
Relative Abundance ◽  
Microbial Population ◽  
Amplicon Sequencing ◽  
Crop Productivity ◽  
Sterile Water ◽  
Tomato Plants ◽  
Operational Taxonomic Units ◽  
16S Rrna Amplicon Sequencing ◽  
Plant Microbiota

Plant microbiota play essential roles in plant health and crop productivity. Comparisons of community composition have suggested seeds, soil, and the atmosphere as reservoirs of phyllosphere microbiota. After finding that leaves of tomato (Solanum lycopersicum) plants exposed to rain carried a higher microbial population size than leaves of tomato plants not exposed to rain, we experimentally tested the hypothesis that rain is a so far neglected reservoir of phyllosphere microbiota. Rain microbiota were thus compared with phyllosphere microbiota of tomato plants either treated with concentrated rain microbiota, filter-sterilized rain, or sterile water. Based on 16S rRNA amplicon sequencing, one-hundred and four operational taxonomic units (OTUs) significantly increased in relative abundance after inoculation with concentrated rain microbiota but no OTU significantly increased after treatment with either sterile water or filter-sterilized rain. Some of the genera to which these 104 OTUs belonged were also found at higher relative abundance on tomatoes exposed to rain outdoors than on tomatoes grown protected from rain in a commercial greenhouse. Taken together, these results point to precipitation as a reservoir of phyllosphere microbiota and show the potential of controlled experiments to investigate the role of different reservoirs in the assembly of phyllosphere microbiota.

Cloacal swabs and alcohol bird specimens are good proxies for compositional analyses of gut microbial communities of Great tits (Parus major)

2019 ◽  
Author(s):  
Kasun H Bodawatta ◽  
Katerina Puzejova ◽  
Katerina Sam ◽  
Michael Poulsen ◽  
Knud A. Jønsson
Keyword(s):  
Microbial Communities ◽  
Digestive Tract ◽  
Wild Bird ◽  
Anthropogenic Impacts ◽  
Parus Major ◽  
Amplicon Sequencing ◽  
Cloacal Swab ◽  
Non Invasive ◽  
16S Rrna Amplicon Sequencing ◽  
Microbiome Research

Abstract Background: Comprehensive studies of wild bird microbiomes are often limited by difficulties of sample acquisition. However, widely used non-invasive cloacal swab methods and under-explored museum specimens preserved in alcohol provide promising avenues to increase our understanding of wild bird microbiomes, provided that they accurately portray natural microbial community compositions. To investigate this assertion, we used 16S rRNA amplicon sequencing of Great tit (Parus major) gut microbiomes to compare 1) microbial communities obtained from dissected digestive tract regions and cloacal swabs, and 2) microbial communities obtained from freshly dissected gut regions and from samples preserved in alcohol for two weeks or two months, respectively. Results: We found no significant differences in alpha diversities in communities of different gut regions and cloacal swabs (except in OTU richness between the dissected cloacal region and the cloacal swabs), or between fresh and alcohol preserved samples. However, we did find significant differences in beta diversity and community composition of cloacal swab samples compared to different gut regions. Despite these quantitative differences, swab samples qualitatively captured the bacterial diversity throughout the gut better than any single compartment. Bacterial community compositions of alcohol-preserved specimens did not differ significantly from freshly dissected samples, although some low-abundant taxa were lost in the alcohol preserved specimens. Conclusions: Our findings suggest that widely used non-invasive cloacal swabs qualitatively depict the gut microbiota composition without having to collect birds to extract the full digestive tract. Secondly, the satisfactory depiction of gut microbial communities in alcohol preserved samples opens up for the possibility of using an enormous resource readily available through museum collections to characterize bird gut microbiomes. The use of extensive museum specimen collections of birds for microbial gut analyses would allow for investigations of temporal patterns of wild bird gut microbiomes, including the potential effects of climate change and anthropogenic impacts. Overall, the utilization of cloacal swabs and museum alcohol specimens can positively impact bird gut microbiome research to help increase our understanding of the role and evolution of wild bird hosts and gut microbial communities.

Non-Normative Events and Family Functioning: The Role of the Family Psychologist

1993 ◽  
Author(s):  
Michele Harway ◽  
◽  
Nancy Boyd-Franklin ◽  
Robert Geffner ◽  
Marsali Hansen ◽  
...  
Keyword(s):  
Family Functioning ◽  
The Family
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