scholarly journals The differences of bacterial communities in the tissues between healthy and diseased Yesso scallop (Patinopecten yessoensis)

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zichao Yu ◽  
Chao Liu ◽  
Qiang Fu ◽  
Guangxia Lu ◽  
Shuo Han ◽  
...  
Keyword(s):  
Carbohydrate Metabolism ◽  
Bacterial Communities ◽  
Prevention And Control ◽  
High Throughput Sequencing ◽  
Northern China ◽  
Adductor Muscle ◽  
Rrna Gene ◽  
Patinopecten Yessoensis ◽  
Yesso Scallop ◽  
And Control

Abstract The tissues of marine invertebrates are colonized by species-rich microbial communities. The dysbiosis of host’s microbiota is tightly associated with the invertebrate diseases. Yesso scallop (Patinopecten yessoensis), one of the most important maricultured scallops in northern China, has recently suffered massive summer mortalities, which causes huge production losses. The knowledge about the interactions between the Yesso scallop and its microbiota is important to develop the strategy for the disease prevention and control. In the present study, the bacterial communities in hemolymph, intestine, mantle and adductor muscle were compared between the healthy and diseased Yesso scallop based on the high-throughput sequencing of 16S rRNA gene. The results indicated obvious difference of the composition rather than the diversity of the bacterial communities between the healthy and diseased Yesso scallop. Vibrio, Francisella and Photobacterium were found to overgrow and dominate in the mantle, adductor muscle and intestine of the diseased scallops, respectively. The prediction of bacterial community metagenomes and the variations of KEGG pathways revealed that the proportions of the pathways related with neurodegenerative diseases and carbohydrate metabolism both increased significantly in the mantle and hemolymph of the diseased scallops. The abundance of the metabolism pathways including carbohydrate metabolism, lipid metabolism and amino acid metabolism decreased significantly in the intestine of diseased scallops. The results suggested that the changes of bacterial communities might be closely associated with the Yesso scallop’s disease, which was helpful for further investigation of the pathogenesis as well as prevention and control of the disease in Yesso scallop.

scholarly journals Multipartner Symbiosis across Biological Domains: Looking at the Eukaryotic Associations from a Microbial Perspective

mSystems ◽  
2019 ◽  
Vol 4 (4) ◽  
Author(s):  
Marta Turon ◽  
Maria J. Uriz ◽  
Daniel Martin
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Marine Invertebrates ◽  
Single Species ◽  
Rrna Gene ◽  
Polychaete Species ◽  
Content Type ◽  
Symbiotic Relationships ◽  
Host Sponge ◽  
Species Specific

ABSTRACTSponges establish tight associations with both micro- and macroorganisms. However, while studies on sponge microbiomes are numerous, nothing is currently known about the microbiomes of sponge-associated polychaetes and their relationships with those of their host sponges. We analyzed the bacterial communities of symbiotic polychaetes (Haplosyllisspp.) and their host sponges (Clathria reinwardti,Amphimedon paraviridis,Neofibularia hartmani, andAaptos suberitoides) to assess the influence of the sponges on the polychaete microbiomes. We identified both eukaryote partners by molecular (16S and COI genes) and morphological features, and we identified their microbial communities by high-throughput sequencing of the 16S rRNA gene (V4 region). We unravel the existence of sixHaplosyllisspecies (five likely undescribed) associated at very high densities with the study sponge species in Nha Trang Bay (central Vietnam). A single polychaete species inhabitedA. paraviridisand was different from the single species that inhabitedA. suberitoides. Conversely, two different polychaete species were found inC. reinwardtiandN. hartmani, depending on the two host locations. Regardless of the host sponge, polychaete microbiomes were species specific, which is a widespread feature in marine invertebrates. More than half of the polychaete bacteria were also found in the host sponge microbiome but at contrasting abundances. Thus, the associated polychaetes seemed to be able to select, incorporate, and enrich part of the sponge microbiome, a selection that appears to be polychaete species specific. Moreover, the bacterial diversity is similar in both eukaryotic partners, which additionally confirms the influence of food (host sponge) on the structure of the polychaete microbiome.IMPORTANCEThe symbiotic lifestyle represents a fundamental cryptic contribution to the diversity of marine ecosystems. Sponges are ideal targets to improve understanding the symbiotic relationships from evolutionary and ecological points of view, because they are the most ancient metazoans on earth, are ubiquitous in the marine benthos, and establish complex symbiosis with both prokaryotes and animals, which in turn also harbor their own bacterial communities. Here, we study the microbiomes of sponge-polychaete associations and confirm that polychaetes feed on their host sponges. The study worms select and enrich part of the sponge microbiome to shape their own species-specific bacterial communities. Moreover, worm microbiome diversity runs parallel to that of its food host sponge. Considering our results on symbiotic polychaetes and previous studies on fishes and mammals, diet appears to be an important source of bacteria for animals to shape their species-specific microbiomes.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2015 ◽  
Vol 12 (13) ◽  
pp. 10233-10269 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Keystone Species ◽  
Small World ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a North–South permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa, and then analyzed these results relative to environmental variables to identify factors controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley, however the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This "small world network" property would render the communities more robust to environmental change but vulnerable to the loss of microbial keystone species.

scholarly journals Prevalence and Genetic Characterization of Cryptosporidium Infection in Java Sparrows (Lonchura oryzivora) in Northern China

2017 ◽  
Vol 2017 ◽  
pp. 1-4 ◽  
Author(s):  
Qiu-Xia Yao ◽  
Xiao-Xuan Zhang ◽  
Kai Chen ◽  
Jian-Gang Ma ◽  
Wen-Bin Zheng ◽  
...  
Keyword(s):  
Pcr Amplification ◽  
Northern China ◽  
Small Subunit ◽  
Rrna Gene ◽  
Ssu Rrna ◽  
Ssu Rrna Gene ◽  
Wide Range ◽  
Baseline Information ◽  
And Control

Cryptosporidiosis is a cosmopolitan parasitosis that affects a wide range of hosts including birds. As information concerning Cryptosporidium in birds is limited, the present study examined the prevalence and genotypes of Cryptosporidium in Java sparrows in Beijing and Shangqiu, northern China. Three hundred and fifty fecal samples were collected from Java sparrows (Lonchura oryzivora, 225 white Java sparrows and 125 gray Java sparrows) in Beijing and Shangqiu in October 2015, and the samples were examined by PCR amplification of the small subunit ribosomal RNA (SSU rRNA) gene. The overall Cryptosporidium prevalence is 13.42% (47/350), with 16.44% (37/225) in white Java sparrows and 8.00% (10/125) in gray Java sparrows. Cryptosporidium prevalence was 9.82% (16/163) in Java sparrows from Beijing and 16.58% (31/187) in Java sparrows from Shangqiu. The prevalence of Cryptosporidium in females and males was 40.63% (26/64) and 7.34% (21/286), respectively. The Cryptosporidium prevalence in Java sparrows of different ages varied from 10.47% to 16.33%. Sequence analysis of the SSU rRNA gene revealed that all the samples represented C. baileyi. This is the first report of Cryptosporidium in gray Java sparrows in China, which extend the host range for C. baileyi. These results provide baseline information for further studies of molecular epidemiology and control of Cryptosporidium infection in poultry in China.

scholarly journals Influence of Heat Events on the Composition of Airborne Bacterial Communities in Urban Ecosystems

2018 ◽  
Vol 15 (10) ◽  
pp. 2295 ◽  
Author(s):  
Zhiguo Fang ◽  
Weijun Guo ◽  
Junwen Zhang ◽  
Xiuqin Lou
Keyword(s):  
High Temperature ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Urban Ecosystems ◽  
Gene Copy ◽  
Airborne Bacteria ◽  
Rrna Gene ◽  
Before And After ◽  
Hot Weather ◽  
Heat Events

Airborne bacteria are significantly affected by meteorological and environmental conditions. However, there is little quantitative data available on the effects of these factors on airborne bacteria in urban ecosystems. In the present study, we analyzed weather-dependent changes in the composition of airborne bacterial communities using high throughput sequencing. Samples were collected before and after a period of constant hot weather at four selected sampling sites (YRBS, ZJGUSJC, TJCR, and BLQG) in Hangzhou. Our results show that the average amount of bacterial 16S rRNA gene copy numbers per m3 of air decreased significantly after constant high temperature. In addition, the number of operational taxonomic units and the Shannon–Wiener diversity indexes of the samples at all four selected sampling sites were significantly decreased after the heat event, showing notable impact on bacterial diversity. We also detected a significant increase in the abundances of spore-forming bacteria. Firmicutes increased from 3.7% to 9.9%, Bacillales increased from 2.6% to 7.6%, and Bacillaceae increased from 1.5% to 5.9%. In addition, we observed an increase in beta-Proteobacteria (18.2% to 50.3%), Rhodocyclaceae (6.9% to 29.9%), and Burkholderiaceae (8.1% to 15.2%). On the other hand, the abundance of alpha-Proteobacteria (39.6% to 9.8%), Caulobacteraceae (17.9% to 0.5%), Sphingomonadaceae (7.2% to 3.3%), and Xanthomonadaceae (3.0% to 0.5%) was significantly lower. Taken together, our data suggest that the composition of airborne bacterial communities varies greatly dependent on heat events, and that such communities include several species that are highly susceptible to high-temperature related stressors such as high air temperature, low relative humidity, and high intensity of solar radiation.

scholarly journals Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes

2016 ◽  
Vol 13 (1) ◽  
pp. 175-190 ◽  
Author(s):  
J. Comte ◽  
C. Lovejoy ◽  
S. Crevecoeur ◽  
W. F. Vincent
Keyword(s):  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Habitat Preferences ◽  
Microbial Consortia ◽  
Rrna Gene ◽  
Permafrost Degradation ◽  
Food Web Structure ◽  
Bacterial Phyla ◽  
Organic Carbon Concentration ◽  
Occurrence Patterns

Abstract. Permafrost thaw ponds and lakes are widespread across the northern landscape and may play a central role in global biogeochemical cycles, yet knowledge about their microbial ecology is limited. We sampled a set of thaw ponds and lakes as well as shallow rock-basin lakes that are located in distinct valleys along a north–south permafrost degradation gradient. We applied high-throughput sequencing of the 16S rRNA gene to determine co-occurrence patterns among bacterial taxa (operational taxonomic units, OTUs), and then analyzed these results relative to environmental variables to identify variables controlling bacterial community structure. Network analysis was applied to identify possible ecological linkages among the bacterial taxa and with abiotic and biotic variables. The results showed an overall high level of shared taxa among bacterial communities within each valley; however, the bacterial co-occurrence patterns were non-random, with evidence of habitat preferences. There were taxonomic differences in bacterial assemblages among the different valleys that were statistically related to dissolved organic carbon concentration, conductivity and phytoplankton biomass. Co-occurrence networks revealed complex interdependencies within the bacterioplankton communities and showed contrasting linkages to environmental conditions among the main bacterial phyla. The thaw pond networks were composed of a limited number of highly connected taxa. This “small world network” property would render the communities more robust to environmental change but vulnerable to the loss of microbial “keystone species”. These highly connected nodes (OTUs) in the network were not merely the numerically dominant taxa, and their loss would alter the organization of microbial consortia and ultimately the food web structure and functioning of these aquatic ecosystems.

scholarly journals Niche specificity and functional diversity of the bacterial communities associated with Ginkgo biloba and Panax quinquefolius

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Hanan R. Shehata ◽  
Subramanyam Ragupathy ◽  
Thomas A. Henry ◽  
Steven G. Newmaster
Keyword(s):  
Functional Diversity ◽  
Ginkgo Biloba ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Alpha Diversity ◽  
Panax Quinquefolius ◽  
Tissue Type ◽  
Rrna Gene ◽  
Associated Bacteria ◽  
Kegg Pathways

AbstractPlant-associated bacteria can establish mutualistic relationships with plants to support plant health. Plant tissues represent heterogeneous niches with distinct characteristics and may thus host distinct microbial populations. The objectives of this study are to investigate the bacterial communities associated with two medicinally and commercially important plant species; Ginkgo biloba and Panax quinquefolius using high Throughput Sequencing (HTS) of 16S rRNA gene, and to evaluate the extent of heterogeneity in bacterial communities associated with different plant niches. Alpha diversity showed that number of operational taxonomic units (OTUs) varied significantly by tissue type. Beta diversity revealed that the composition of bacterial communities varied between tissue types. In Ginkgo biloba and Panax quinquefolius, 13% and 49% of OTUs, respectively, were ubiquitous in leaf, stem and root. Proteobacteria, Bacteroidetes, Actinobacteria and Acidobacteria were the most abundant phyla in Ginkgo biloba while Proteobacteria, Bacteroidetes, Actinobacteria, Plantomycetes and Acidobacteria were the most abundant phyla in Panax quinquefolius. Functional prediction of these bacterial communities using MicrobiomeAnalyst revealed 5843 and 6251 KEGG orthologs in Ginkgo biloba and Panax quinquefolius, respectively. A number of these KEGG pathways were predicted at significantly different levels between tissues. These findings demonstrate the heterogeneity, niche specificity and functional diversity of plant-associated bacteria.

scholarly journals Culture-independent analysis of the bacterial communities in Chinese fermented vegetables and genomic analysis of lactic acid bacteria

2021 ◽  
Author(s):  
Jianming Zhang ◽  
Hye Seon Song ◽  
Chengcheng Zhang ◽  
Yeon Bee Kim ◽  
Seong Woon Roh ◽  
...  
Keyword(s):  
Lactic Acid ◽  
Lactic Acid Bacteria ◽  
Bacterial Communities ◽  
High Throughput Sequencing ◽  
Rrna Gene ◽  
Bacterial Strains ◽  
Whole Genome Analysis ◽  
Sequencing Platform ◽  
Tuber Mustard ◽  
Fermented Vegetables

Abstract Six different fermented vegetables were collected from Zhejiang Province, China, to explore the associated bacterial communities using a high-throughput sequencing platform. A total of 24 phyla, 274 families and 569 genera were identified from six samples. Firmicutes and Proteobacteria were the main phyla in all of samples. Meanwhile, Brevibacterium was the major genus in Xiaoshan pickled radish. Lactobacillus-related genera and Vibrio were the major genera in fermented potherb mustard and its brine. Enterobacter and Cobetia were the major genera in fermented radish and its brine. Chromohalobacter was the major genus in the tuber mustard. These results indicated there were clear differences between the bacterial genera present in Xiaoshan pickled radish, fermented potherb mustard, fermented radish, and tuber mustard. This demonstrated the possible influences of raw materials and manufacturing processes. Furthermore, a large number of lactic acid bacteria were isolated and identified by culture-dependent and 16S rRNA gene sequence analysis, which accounted for more than 68% of all the isolates. In addition, whole genome analysis of Lactobacillus suantsaii, Lactobacillus sakei subsp. sakei, and Weissella cibaria showed they had large numbers of genes associated with carbohydrate metabolism. This may explain why these three bacterial strains can grow in fermented vegetable environments.

scholarly journals An Oligosaccharide Rich Diet Increases Akkermansia spp. Bacteria in the Equine Microbiota

2021 ◽  
Vol 12 ◽  
Author(s):  
Frederikke Christine Lindenberg ◽  
Ditte Olsen Lützhøft ◽  
Lukasz Krych ◽  
James Fielden ◽  
Witold Kot ◽  
...  
Keyword(s):  
Gut Microbiota ◽  
Immune Responses ◽  
High Throughput Sequencing ◽  
Post Partum ◽  
Bacterial Species ◽  
Test Group ◽  
Fecal Microbiota ◽  
Rrna Gene ◽  
Anti Inflammatory ◽  
And Control

Some oligosaccharides induce growth of anti-inflammatory bacterial species and induce regulatory immunity in humans as well as animals. We have shown that the equine gut microbiota and the immune-microbial homeostasis largely stabilize within the first 50 days of life. Furthermore, we have previously established that certain bacterial species in the equine gut correlated with regulatory immunity. Accordingly, we hypothesized that an oligosaccharide rich diet fed to foals during the first 50 days would increase the abundance of bacterial species associated with regulatory immunity, and that this would influence immune responses in the foals. Eight pregnant mares and their foals were fed an oligosaccharide rich diet from 4 weeks before expected parturition until 49 days post-partum. Six mares and foals served as control. Fecal microbiota from mares and foals was characterized using 16S rRNA gene amplicon high throughput sequencing. On Day 49 the test foals had significantly higher abundances of Akkermansia spp. Blood sampled from the foals in the test group on Day 7, 28, and 49 showed non-significant increases in IgA, and decreases in IgG on Day 49. In BALB/cBomTac mice inoculated with gut microbiota from test and control foals we found increased species richness, increased relative abundance of several species identified as potentially anti-inflammatory in horses, which were unclassified Clostridiales, Ruminococcaceae, Ruminococcus, Oscilospira, and Coprococcus. We also found increased il10 expression in the ileum if inoculated with test foal microbiota. We conclude that an oligosaccharide diet fed to foals in the “window of opportunity,” the first 50 days of life, increases the abundance of anti-inflammatory species in the microbiota with potentially anti-inflammatory effects on regulatory immunity.

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