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

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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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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Metagenomic Exploration of Bacterial Community Structure of Earthworms’ Gut

Journal of Pure and Applied Microbiology ◽

10.22207/jpam.15.3.05 ◽

2021 ◽

Author(s):

Samrendra Singh Thakur ◽

Azhar Rashid Lone ◽

Nalini Tiwari ◽

Subodh Kumar Jain ◽

Shweta Yadav

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Community Structure ◽

Alpha Diversity ◽

Eudrilus Eugeniae ◽

Phenotypic Analysis ◽

Perionyx Excavatus ◽

Gram Negative ◽

Earthworm Species

Living organisms are naturally bestowed with unique and imitable qualities for maintaining ecological balance and earthworms are no exceptions. These so-called keystone species of terrestrial ecosystems are equipped with wonderful machinery, allowing them to nurture soil beautifully. Earthworm gut represents a potential microbial reservoir, having a complex interdependence with the host. The study aimed to profile bacterial community structure of three earthworm species belonging to two different life forms; Perionyx excavatus and Eudrilus eugeniae (epigeic), Polypheretima elongata (endogeic) respectively. Diversity analysis using 16S amplicon sequencing revealed that the dominant phyla were Proteobacteria (34.17-77.88) followed by Actinobacteria (13.43-35.54%), Firmicutes (1.69-15.45%) and Bacteroidetes (0.51-8.12%). The alpha diversity indices explicit similar gut microbiota of Perionyx excavatus and Eudrilus eugeniae and while higher alpha diversity was recorded in comparison to Polypheretima elongata gut. The taxonomic to the phenotypic annotation of 16S rRNA metagenomes revealed that dominance of Gram-negative bacterial community in all earthworm species while, Polypheretima elongata comprises higher percentage (78%) of Gram-negative bacterial community to Perionyx excavatus (32.3%) and Eudrilus eugeniae (38.3%). The oxygen requirement phenotypic analysis showed that all earthworm species were abundant with aerobic followed by anaerobic bacterial groups. Furthermore, functional metabolism phenotypic analysis revealed that a high abundance of ammonia oxidizers (29.3-80.2%), the gut microbiomes showed the relative abundance of sulphate reducer (22.6-78.7%), nitrite reducer (19.8-73.2%), dehalogenators (12.6-25.1%), illustrating in the role of these microbial communities in various degradation and bioremediation processes. The present study signifies the intrinsic gut microbiota of earthworm species for intensified biodegradation.

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Gut microbiota relationships to lung function and adult asthma phenotype: a pilot study

BMJ Open Respiratory Research ◽

10.1136/bmjresp-2018-000324 ◽

2018 ◽

Vol 5 (1) ◽

pp. e000324 ◽

Cited By ~ 10

Author(s):

Lesa Begley ◽

Siddharth Madapoosi ◽

Kristopher Opron ◽

Ogechukwu Ndum ◽

Alan Baptist ◽

...

Keyword(s):

Community Structure ◽

Pilot Study ◽

Lung Function ◽

Bacterial Community ◽

Gut Microbiota ◽

Bacterial Community Structure ◽

Forced Expiratory Volume ◽

Asthma Phenotype ◽

Paired Samples ◽

Compositional Stability

IntroductionDespite strong evidence that maturation patterns of the gut microbiome in early life influence the risk for childhood asthma, very little is known about gut microbiota patterns in adults with established asthma, and of greater interest relationships to phenotypic features that characterise asthma heterogeneity.MethodsFifty-eight faecal samples from 32 adults with (n=24) and without (n=8) asthma were analysed using 16S ribosomal RNA gene sequencing methods to characterise intestinal bacterial composition. Compositional stability of paired samples was evaluated and features of gut bacterial community structure analysed in relation to extensive clinical characterisation data collected from subjects, who were enrolled in a prospective observational cohort study at the University of Michigan.ResultsDifferences in gut bacterial community structure were associated with aeroallergen sensitisation and lung function as assessed by forced expiratory volume in 1 s (FEV1) %predicted. Associations with FEV1 were consistently observed across independent analytic approaches. k-means clustering of the gut microbiota data in subjects with asthma revealed three different clusters, distinguished most strongly by FEV1 (p<0.05) and trends in differences in other clinical and inflammatory features.ConclusionIn this pilot study of asthmatic and non-asthmatic subjects, significant relationships between gut microbiota composition, aeroallergen sensitisation and lung function were observed. These preliminary findings merit further study in larger cohorts to explore possible mechanistic links to asthma phenotype.

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

10.1101/2021.03.30.437633 ◽

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.

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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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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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Different techniques for high‐throughput amplicon sequencing of the soil bacterial community structure after spring maize cultivation

Soil Use and Management ◽

10.1111/sum.12617 ◽

2020 ◽

Author(s):

Yue Yang ◽

Yan‐an Tong ◽

Dave Chadwick ◽

Lian‐you Liang ◽

Hong‐chang Li ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

High Throughput ◽

Bacterial Community Structure ◽

Amplicon Sequencing ◽

Soil Bacterial Community ◽

Spring Maize ◽

Soil Bacterial Community Structure ◽

Maize Cultivation ◽

Soil Bacterial

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Dietary Supplementation with Fermented Brassica rapa L. Stimulates Defecation Accompanying Change in Colonic Bacterial Community Structure

Nutrients ◽

10.3390/nu13061847 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1847

Author(s):

Sachi Tanaka ◽

Kana Yamamoto ◽

Chisato Hamajima ◽

Fuka Takahashi ◽

Katsunori Endo ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Gut Microbiota ◽

Immune Responses ◽

Brassica Rapa ◽

Bacterial Community Structure ◽

Intervention Study ◽

Bacterial Community Composition ◽

Defecation Frequency ◽

Fecal Bacterial Community

Our previous studies have elucidated that oral administration of Brassica rapa L. extract, known as Nozawana in Japan, alters immune responses and gut microbiota composition, increasing the numbers of butyrate-producing bacteria. Therefore, further investigation would help elucidate the mechanism attributable for the changes and health-promoting effects observed after B rapa L. extract ingestion. To reveal the modulation effects of fermented B. rapa L. on immune function and intestinal bacterial community structure, we conducted an intervention study with healthy volunteers followed by a mouse feeding study. The pilot intervention study was conducted for healthy volunteers aged 40–64 years under the hypothesis that the number of subjects exhibiting any change in gut microbiota in response to fermented B. rapa L. consumption may be limited. In total, 20 volunteers consumed 30 g of fermented B. rapa L. per day for 4 weeks. The fecal bacterial community composition of the volunteers was characterized using terminal-restriction fragment length polymorphism patterning followed by clustering analysis. To evaluate the detailed changes in the immune responses and the gut bacterial composition, assessed by high-throughput sequencing, we fed healthy mice with freeze-dried, fermented B. rapa L. for 2 weeks. The fecal bacterial community composition of the volunteers before the intervention was divided into three clades. Regardless of the clade, the defecation frequency significantly increased during the intervention weeks compared with that before the intervention. However, this clustering detected a specific increase of Prevotella in one cluster (low to zero Prevotella and high occupation of Clostridium at clusters IV and XIVa) post-ingestion. The cytokine production of spleen cells significantly increased due to feeding fermented B. rapa L. to the mice. This supplementary in vivo trial provided comparable results to the volunteer study regarding the effects of ingestion of the material given the compositional change complying with that of dietary fiber, particularly in the increase of genera Prevotella, Lachnospira, and genera in the Ruminococcaceae family, and the increase in daily defecation amount during 2 weeks of administration. We conclude that feeding fermented B. rapa L. may be responsible for the observed modulation in gut microbiota to increase fiber-degrading bacteria and butyrate-producing bacteria which may be relevant to the improvement in bowel function such as defecation frequency.

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