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

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.

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Diet is not the primary driver of bacterial community structure in the gut of litter-feeding cockroaches

BMC Microbiology ◽

10.1186/s12866-019-1601-9 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 5

Author(s):

Niclas Lampert ◽

Aram Mikaelyan ◽

Andreas Brune

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Community Structure ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Feeding Groups ◽

Reducing Conditions ◽

Primary Driver

Abstract Background Diet is a major determinant of bacterial community structure in termite guts, but evidence of its importance in the closely related cockroaches is conflicting. Here, we investigated the ecological drivers of the bacterial gut microbiota in cockroaches that feed on lignocellulosic leaf litter. Results The physicochemical conditions determined with microsensors in the guts of Ergaula capucina, Pycnoscelus surinamensis, and Byrsotria rothi were similar to those reported for both wood-feeding and omnivorous cockroaches. All gut compartments were anoxic at the center and showed a slightly acidic to neutral pH and variable but slightly reducing conditions. Hydrogen accumulated only in the crop of B. rothi. High-throughput amplicon sequencing of bacterial 16S rRNA genes documented that community structure in individual gut compartments correlated strongly with the respective microenvironmental conditions. A comparison of the hindgut microbiota of cockroaches and termites from different feeding groups revealed that the vast majority of the core taxa in cockroaches with a lignocellulosic diet were present also in omnivorous cockroaches but absent in wood-feeding higher termites. Conclusion Our results indicate that diet is not the primary driver of bacterial community structure in the gut of wood- and litter-feeding cockroaches. The high similarity to the gut microbiota of omnivorous cockroaches suggests that the dietary components that are actually digested do not differ fundamentally between feeding groups.

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Assessment of total bacterial diversity in whiteleg shrimps and its aquaculture environment in Pangkajene and Banyuwangi, Indonesia

Asia Pacific Journal of Molecular Biology and Biotechnology ◽

10.35118/apjmbb.2021.029.3.04 ◽

2021 ◽

pp. 26-37

Author(s):

Yuni Puji Hastuti ◽

Yuli Siti Fatma ◽

Hardi Pitoyo ◽

Wildan Nurussalam ◽

Jajang Ruhyana

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Bacterial Community Structure ◽

Amplicon Sequencing ◽

16S Rrna Genes ◽

Rrna Genes ◽

Bacterial Composition ◽

Sequencing Platform ◽

The Difference

Detection of bacterial diversity in whiteleg shrimps and its rearing water is a vital first step in monitoring aquaculture activities. Bacterial community imbalance in whiteleg shrimps and its rearing water influences the quality and quantity of shrimp production. Identifying the bacterial community provides basic information related to dominant bacterial groups in whiteleg shrimps and environments, providing recommendations for proper environmental monitoring and management. In this study, we investigated bacterial community structure in the rearing water and intestinal tract of whiteleg shrimp (Litopenaeus vannamei) collected from two sites, i.e., Pangkajene, South Sulawesi (SU) and Banyuwangi, East Java (BW), Indonesia. The bacterial community was analyzed using amplicon sequencing with Illumina sequencing platform based on the V3-V4 region of the 16S rRNA genes. Bacterial diversity and composition were found differed between the rearing water and the shrimps’ intestines. Bacterial diversity in the rearing water of Banyuwangi (W.BW) was higher than that of Pangkajene (W.SU). Proteobacteria, Bacteroidetes, and Firmicutes were found as the most dominant phyla in rearing water from both farms, while distinct bacterial composition was observed in the shrimps’ intestines. The shrimp intestine from Banyuwangi (U.BW) was dominated by Firmicutes (22.36%), Proteobacteria (22.33%), and Verrucomicrobia (21.11%). In contrast, the shrimp intestine from Pangkajene (U.SU) was highly dominated by Tenericutes (88.54%), followed by Proteobacteria (4.66%), and Firmicutes (2.27%). The difference in bacterial community structure between the rearing water and shrimps’ intestines suggested that the host intestinal environment might have greater selective pressure for bacterial composition inhabiting L.vannamei intestines. Our observations suggest that the shrimps cultured in the rearing water with the similar dominant bacterial group have specific intestinal bacterial diversity.

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Microbial taxa in dust and excreta associated with the productive performance of commercial meat chicken flocks

Animal Microbiome ◽

10.1186/s42523-021-00127-y ◽

2021 ◽

Vol 3 (1) ◽

Author(s):

Yugal Raj Bindari ◽

Robert J. Moore ◽

Thi Thu Hao Van ◽

Stephen W. Walkden-Brown ◽

Priscilla F. Gerber

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Community Structure ◽

Population Level ◽

Amplicon Sequencing ◽

Feed Conversion ◽

High Performing ◽

Low Performance ◽

Feed Conversion Rate

Abstract Background A major focus of research on the gut microbiota of poultry has been to define signatures of a healthy gut and identify microbiota components that correlate with feed conversion. However, there is a high variation in individual gut microbiota profiles and their association with performance. Population level samples such as dust and pooled excreta could be useful to investigate bacterial signatures associated with productivity at the flock-level. This study was designed to investigate the bacterial signatures of high and low-performing commercial meat chicken farms in dust and pooled excreta samples. Poultry house dust and fresh pooled excreta were collected at days 7, 14, 21, 28 and 35 of age from 8 farms of two Australian integrator companies and 389 samples assessed by 16S ribosomal RNA gene amplicon sequencing. The farms were ranked as low (n = 4) or high performers (n = 4) based on feed conversion rate corrected by body weight. Results Permutational analysis of variance based on Bray–Curtis dissimilarities using abundance data for bacterial community structure results showed that company explained the highest variation in the bacterial community structure in excreta (R2 = 0.21, p = 0.001) while age explained the highest variation in the bacterial community structure in dust (R2 = 0.13, p = 0.001). Farm performance explained the least variation in the bacterial community structure in both dust (R2 = 0.03, p = 0.001) and excreta (R2 = 0.01, p = 0.001) samples. However, specific bacterial taxa were found to be associated with high and low performance in both dust and excreta. The bacteria taxa associated with high-performing farms in dust or excreta found in this study were Enterococcus and Candidatus Arthromitus whereas bacterial taxa associated with low-performing farms included Nocardia, Lapillococcus, Brachybacterium, Ruania, Dietzia, Brevibacterium, Jeotgalicoccus, Corynebacterium and Aerococcus. Conclusions Dust and excreta could be useful for investigating bacterial signatures associated with high and low performance in commercial poultry farms. Further studies on a larger number of farms are needed to determine if the bacterial signatures found in this study are reproducible.

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Bacterial community structure and response to nitrogen amendments in Lake Shenandoah (VA, USA)

Water Science & Technology ◽

10.2166/wst.2019.311 ◽

2019 ◽

Vol 80 (4) ◽

pp. 675-684

Author(s):

G. Reynoso ◽

M. R. Smith ◽

C. P. Holmes ◽

C. R. Keelan ◽

S. E. McGrath ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Community Structure ◽

Nitrogen Sources ◽

Amplicon Sequencing ◽

Freshwater Ecosystems ◽

Nitrogen Loading ◽

Significant Shift ◽

Nitrogen And Phosphorus ◽

The Impact

Abstract Microbial processes are critical to the function of freshwater ecosystems, yet we still do not fully understand the factors that shape freshwater microbial communities. Furthermore, freshwater ecosystems are particularly susceptible to effects of environmental change, including influx of exogenous nutrients such as nitrogen and phosphorus. To evaluate the impact of nitrogen loading on the microbial community structure of shallow freshwater lakes, water samples collected from Lake Shenandoah (Virginia, USA) were incubated with two concentrations of either ammonium, nitrate, or urea as a nitrogen source. The potential impact of these nitrogen compounds on the bacterial community structure was assessed via 16S rRNA amplicon sequencing. At the phylum level, the dominant taxa in Lake Shenandoah were comprised of Actinobacteria and Proteobacteria, which were not affected by exposure to the various nitrogen treatments. Overall, there was not a significant shift in the diversity of the bacterial community of Lake Shenandoah with the addition of nitrogen sources, indicating this shallow system may be constrained by other environmental factors.

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Divergence in Gut Bacterial Community Among Life Stages of the Rainbow Stag Beetle Phalacrognathus muelleri (Coleptera: Lucanidae)

Insects ◽

10.3390/insects11100719 ◽

2020 ◽

Vol 11 (10) ◽

pp. 719

Author(s):

Miaomiao Wang ◽

Xingjia Xiang ◽

Xia Wan

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Community Composition ◽

Bacterial Community Structure ◽

High Throughput Sequencing ◽

Bacterial Community Composition ◽

Alpha Diversity ◽

Illumina Miseq ◽

Life Stages ◽

Early Instar

Although stag beetles are popular saprophytic insects, there are few studies about their gut bacterial community. This study focused on the gut bacterial community structure of the rainbow stag beetle (i.e., Phalacrognathus muelleri) in its larvae (three instars) and adult stages, using high throughput sequencing (Illumina Miseq). Our aim was to compare the gut bacterial community structure among different life stages. The results revealed that bacterial alpha diversity increased from the 1st instar to the 3rd instar larvae. Adults showed the lowest gut bacterial alpha diversity. Bacterial community composition was significantly different between larvae and adults (p = 0.001), and 1st instar larvae (early instar) had significant differences with the 2nd (p= 0.007) and 3rd (p = 0.001) instar larvae (final instar). However, there was little difference in the bacterial community composition between the 2nd and 3rd instar larvae (p = 0.059). Our study demonstrated dramatic shifts in gut bacterial community structure between larvae and adults. Larvae fed on decaying wood and adults fed on beetle jelly, suggesting that diet is a crucial factor shaping the gut bacterial community structure. There were significant differences in bacterial community structure between early instar and final instars larvae, suggesting that certain life stages are associated with a defined gut bacterial community.

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