Bacterial Composition and Diversity of the Digestive Tract of Odontomachus monticola Emery and Ectomomyrmex javanus Mayr

Ponerine ants are generalist predators feeding on a variety of small arthropods, annelids, and isopods; however, knowledge of their bacterial communities is rather limited. This study investigated the bacterial composition and diversity in the digestive tract (different gut sections and the infrabuccal pockets (IBPs)) of two ponerine ant species (Odontomachus monticola Emery and Ectomomyrmex javanus Mayr) distributed in northwestern China using high-throughput sequencing. We found that several dominant bacteria that exist in other predatory ants were also detected in these two ponerine ant species, including Wolbachia, Mesoplasma, and Spiroplasma. Bacterial communities of these two ant species were differed significantly from each other, and significant differences were also observed across their colonies, showing distinctive inter-colony characteristics. Moreover, bacterial communities between the gut sections (crops, midguts, and hindguts) of workers were highly similar within colony, but they were clearly different from those in IBPs. Further, bacterial communities in the larvae of O. monticola were similar to those in the IBPs of workers, but significantly different from those in gut sections. We presume that the bacterial composition and diversity in ponerine ants are related to their social behavior and feeding habits, and bacterial communities in the IBPs may play a potential role in their social life.

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New Insights on the Zeugodacus cucurbitae (Coquillett) Bacteriome

Microorganisms ◽

10.3390/microorganisms9030659 ◽

2021 ◽

Vol 9 (3) ◽

pp. 659

Author(s):

Elias Asimakis ◽

Panagiota Stathopoulou ◽

Apostolis Sapounas ◽

Kanjana Khaeso ◽

Costas Batargias ◽

...

Keyword(s):

Relative Abundance ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Mutual Exclusion ◽

Bacterial Composition ◽

Operational Taxonomic Units ◽

Host Diet ◽

Dominant Bacteria ◽

High Degree

Various factors, including the insect host, diet, and surrounding ecosystem can shape the structure of the bacterial communities of insects. We have employed next generation, high-throughput sequencing of the 16S rRNA to characterize the bacteriome of wild Zeugodacus (Bactrocera) cucurbitae (Coquillett) flies from three regions of Bangladesh. The tested populations developed distinct bacterial communities with differences in bacterial composition, suggesting that geography has an impact on the fly bacteriome. The dominant bacteria belonged to the families Enterobacteriaceae, Dysgomonadaceae and Orbaceae, with the genera Dysgonomonas, Orbus and Citrobacter showing the highest relative abundance across populations. Network analysis indicated variable interactions between operational taxonomic units (OTUs), with cases of mutual exclusion and copresence. Certain bacterial genera with high relative abundance were also characterized by a high degree of interactions. Interestingly, genera with a low relative abundance like Shimwellia, Gilliamella, and Chishuiella were among those that showed abundant interactions, suggesting that they are also important components of the bacterial community. Such knowledge could help us identify ideal wild populations for domestication in the context of the sterile insect technique or similar biotechnological methods. Further characterization of this bacterial diversity with transcriptomic and metabolic approaches, could also reveal their specific role in Z. cucurbitae physiology.

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Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

10.21203/rs.3.rs-29755/v1 ◽

2020 ◽

Author(s):

Zongfu Hu ◽

Deying Ma ◽

huaxin Niu ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

High Throughput ◽

Bacterial Communities ◽

Crude Protein ◽

High Throughput Sequencing ◽

Ammonium N ◽

Enzyme Combination ◽

Fermentation Quality ◽

Dominant Bacteria

Abstract This study aimed to evaluate the effects of enzymes (cellulase combined with galactosidase),, and the combination of these enzymes with Lactobacillus plantarum (LP) on bacterial diversity using high-throughput sequencing. Alfalfa forages were treated without or with cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), ɑ-galactosidase + LP (GALP). After 56 days of ensiling, All the treated silages exhibited improved fermentation quality as reflecting by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage. Enzymatic treatment improved nutrients value by increased the level of crude protein and decreased the neutral detergent fibre (NDF) level. Treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. LAB dominated the bacterial community of the treated silage after ensiling. The dominant bacteria from Garciella, Enterococcus, Lactobacillus and Pediococcus in control silage changed to Lactobacillus and Pediococcus in CEGA silage, and Lactobacillus in CELP and GALP silages. Collectively, enzymes and enzyme in combination with inoculants both greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus in enzymes only silge (CEGA) and Lactobacillus in enzyme combination with inoculants silage (CELP and GALP).

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Effects of different vegetable rotations on the rhizosphere bacterial community and tomato growth in a continuous tomato cropping substrate

PLoS ONE ◽

10.1371/journal.pone.0257432 ◽

2021 ◽

Vol 16 (9) ◽

pp. e0257432

Author(s):

Li Jin ◽

Jian Lyu ◽

Ning Jin ◽

Jianming Xie ◽

Yue Wu ◽

...

Keyword(s):

Community Structure ◽

Bacterial Community ◽

Bacterial Diversity ◽

Crop Rotation ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Total N ◽

Rhizosphere Bacterial Community ◽

Healthy Growth ◽

Dominant Bacteria

In this study, High throughput sequencing was used to analyze the effects of different vegetable rotations on the rhizosphere bacterial diversity and community structure in a substrate that was used for continuous tomato cropping (CK). The vegetable rotations tested were cabbage/tomato (B), kidney bean/tomato (D), and celery/tomato (Q). The results revealed that the substrate bacterial diversity and richness of each crop rotation were higher than those of CK. The highest bacterial diversity was found in the B substrate, followed by the Q and D substrates. Further comparison showed that the rhizosphere bacterial community structure of Q substrate was significantly different to that of CK. Compared with the CK, the Q substrate had a significantly higher relative abundance of several dominant microflora, such as Acidobacteria, Chloroflexi, and Firmicutes. Additionally, the Q rotation significantly increased the abundance of beneficial bacteria, such as Actinobacteria_unclassified and Anaerolineaceae_unclassified. A redundancy analysis showed that Most dominant bacteria correlated positively with the substrate pH, total N, and alkali-hydrolyzable N but negatively with the available P, available K, total P, total K, and organic matter contents and substrate EC. The substrates after crop rotation improved the growth and physiological condition of the subsequent tomato plants, among which those from the Q rotation performed the best. Therefore, celery rotation not only increased the richness and diversity of bacterial communities in the substrate but also significantly increased the richness of the beneficial bacterial communities, allowing better maintenance of the substrate microenvironment for the healthy growth of crops.

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Gut microbiota variations in a rescued spotted seal Phoca largha pup

Aquatic Biology ◽

10.3354/ab00729 ◽

2020 ◽

Vol 29 ◽

pp. 105-109

Author(s):

J Tian ◽

J Du ◽

J Han ◽

Z Wang ◽

Z Fu ◽

...

Keyword(s):

Gut Microbiota ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Gut Health ◽

Conservation Action ◽

Spotted Seal ◽

Phoca Largha ◽

Host Health ◽

In Captivity ◽

Dominant Bacteria

Rescuing seal pups is an important conservation action for spotted seals Phoca largha. Gut microbiota are directly associated with host health and diet metabolism. Therefore, knowledge gained from gut microbiota variations of spotted seal pups held in captivity after rescue can help formulate comprehensive rescue plans for the future. In this study, we collected feces from a rescued spotted seal pup every 3 d during the rescue process. Fecal bacterial communities were measured by high-throughput sequencing based on 16S rRNA amplification. Firmicutes were the most dominant bacteria, comprising >70% of the total gut microbiota. Moreover, differences in fecal bacterial communities of the rescued spotted seal pup between rescue and release were compared. At release, the abundances of 2 potential bacteria related to gut health, Blautia producta and Cetobacterium somerae, were remarkably lower, while Clostridium perfringens, a key mammalian pathogen, was significantly higher in the feces of the released pup. Moreover, the pup experienced a bout of diarrhea during its time in captivity, which resulted in a momentary change in its gut microbiota. Fusobacterium was recognized as a potential causative pathogen for the diarrhea. This study contributes to our understanding of gut microbiota variations in spotted seal pups during the rescue period.

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Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

AMB Express ◽

10.1186/s13568-020-01158-5 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Zongfu Hu ◽

Deying Ma ◽

Huaxin Niu ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

Bacterial Communities ◽

Crude Protein ◽

High Throughput Sequencing ◽

Protein Levels ◽

Nutrient Value ◽

Ammonium N ◽

Fermentation Quality ◽

Dominant Bacteria

AbstractThe goal of the present study was to evaluate the effects of enzymes (cellulase combined with galactosidase) and their combination with Lactobacillus plantarum (LP) on bacterial diversity in alfalfa silages using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage (P < 0.05). Enzymatic treatment improved nutrient value by increasing crude protein levels and decreasing neutral detergent fibre (NDF) levels (P < 0.05). Silage treatment significantly altered the bacterial community, as determined by PCoA (P < 0.05). Lactic acid bacteria (LAB) dominated the bacterial community of the treated silage after ensiling. The dominant bacteria changed from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage to Lactobacillus and Pediococcus in the CEGA silage and Lactobacillus in the CELP and GALP silages. Collectively, these results suggest that treatment with both enzymes alone and in combination with inoculants greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus observed in the silage treated with enzymes alone (CEGA) and Lactobacillus observed in the silage treated with a combination of enzymes and inoculants (CELP and GALP).

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Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

10.21203/rs.3.rs-29755/v2 ◽

2020 ◽

Author(s):

Zongfu hu ◽

Deying Ma ◽

Huaxin Niu ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

High Throughput ◽

Bacterial Communities ◽

Crude Protein ◽

High Throughput Sequencing ◽

Nutrient Value ◽

Ammonium N ◽

Fermentation Quality ◽

Dominant Bacteria

Abstract This study aimed to evaluate the effects of enzymes (cellulase combined with galactosidase), and the combination of these enzymes with Lactobacillus plantarum (LP) on bacterial diversity using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all the treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage. Enzymatic treatment improved nutrient value by increasing the level of crude protein and decreasing the neutral detergent fibre (NDF) level. Treatment of the silage significantly changed the bacterial community, as determined by the PCoA test. LAB dominated the bacterial community of the treated silage after ensiling. The dominant bacteria from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage changed to Lactobacillus and Pediococcus in the CEGA silage, and Lactobacillus in the CELP and GALP silages. Collectively, enzymes and enzymes in combination with inoculants both greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus in the silage with enzymes only (CEGA) and Lactobacillus in the silage with a combination of enzymes and inoculants (CELP and GALP).

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Enzyme additives influence bacterial communities of Medicago sativa silage as determined by Illumina sequencing

10.21203/rs.3.rs-29755/v3 ◽

2020 ◽

Author(s):

zongfu hu ◽

Deying Ma ◽

huaxin Niu ◽

Jie Chang ◽

Jianhua Yu ◽

...

Keyword(s):

Lactic Acid ◽

Bacterial Community ◽

Bacterial Communities ◽

Crude Protein ◽

High Throughput Sequencing ◽

Protein Levels ◽

Nutrient Value ◽

Ammonium N ◽

Fermentation Quality ◽

Dominant Bacteria

Abstract The goal of the present study was to evaluate the effects of enzymes (cellulase combined with galactosidase) and their combination with Lactobacillus plantarum (LP) on bacterial diversity in alfalfa silages using high-throughput sequencing. Alfalfa forages were treated with or without cellulase + ɑ-galactosidase (CEGA), cellulase + LP (CELP), or ɑ-galactosidase + LP (GALP). After 56 days of ensiling, all treated silages exhibited improved fermentation quality, as reflected by decreased pH, ammonium-N and increased lactic acid levels compared to the control silage (P < 0.05). Enzymatic treatment improved nutrient value by increasing crude protein levels and decreasing neutral detergent fibre (NDF) levels (P < 0.05). Silage treatment significantly altered the bacterial community, as determined by PCoA (P < 0.05). Lactic acid bacteria (LAB) dominated the bacterial community of the treated silage after ensiling. The dominant bacteria changed from Garciella, Enterococcus, Lactobacillus and Pediococcus in the control silage to Lactobacillus and Pediococcus in the CEGA silage and Lactobacillus in the CELP and GALP silages. Collectively, these results suggest that treatment with both enzymes alone and in combination with inoculants greatly increased the abundance of LAB, with Enterococcus, Lactobacillus and Pediococcus observed in the silage treated with enzymes alone (CEGA) and Lactobacillus observed in the silage treated with a combination of enzymes and inoculants (CELP and GALP).

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Effects of a Bioprocessed Soybean Meal Ingredient on the Intestinal Microbiota of Hybrid Striped Bass, Morone chrysops x M. saxatilis

Microorganisms ◽

10.3390/microorganisms9051032 ◽

2021 ◽

Vol 9 (5) ◽

pp. 1032

Author(s):

Emily Celeste Fowler ◽

Prakash Poudel ◽

Brandon White ◽

Benoit St-Pierre ◽

Michael Brown

Keyword(s):

Striped Bass ◽

Soybean Meal ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Rrna Gene ◽

Hybrid Striped Bass ◽

Bacterial Composition ◽

Morone Chrysops ◽

Fish Diets ◽

Significant Difference

The hybrid striped bass (Morone chrysops x M. saxatilis) is a carnivorous species and a major product of US aquaculture. To reduce costs and improve resource sustainability, traditional ingredients used in fish diets are becoming more broadly replaced by plant-based products; however, plant meals can be problematic for carnivorous fish. Bioprocessing has improved nutritional quality and allowed higher inclusions in fish diets, but these could potentially affect other systems such as the gut microbiome. In this context, the effects of bioprocessed soybean meal on the intestinal bacterial composition in hybrid striped bass were investigated. Using high-throughput sequencing of amplicons targeting the V1–V3 region of the 16S rRNA gene, no significant difference in bacterial composition was observed between fish fed a control diet, and fish fed a diet with the base bioprocessed soybean meal. The prominent Operational Taxonomic Unit (OTU) in these samples was predicted to be a novel species affiliated to Peptostreptococcaceae. In contrast, the intestinal bacterial communities of fish fed bioprocessed soybean meal that had been further modified after fermentation exhibited lower alpha diversity (p < 0.05), as well as distinct and more varied composition patterns, with OTUs predicted to be strains of Lactococcus lactis, Plesiomonas shigelloides, or Ralstonia pickettii being the most dominant. Together, these results suggest that compounds in bioprocessed soybean meal can affect intestinal bacterial communities in hybrid striped bass.

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Exploring the Bacterial Communities of Infernaccio Waterfalls: A Phenotypic and Molecular Characterization of Acinetobacter and Pseudomonas Strains Living in a Red Epilithic Biofilm

Diversity ◽

10.3390/d11100175 ◽

2019 ◽

Vol 11 (10) ◽

pp. 175 ◽

Cited By ~ 1

Author(s):

Carolina Chiellini ◽

Sofia Chioccioli ◽

Alberto Vassallo ◽

Stefano Mocali ◽

Elisangela Miceli ◽

...

Keyword(s):

Heavy Metals ◽

Bacterial Communities ◽

High Throughput Sequencing ◽

Rapd Analysis ◽

Environmental Pollutants ◽

Biotechnological Applications ◽

Bacterial Strains ◽

Bacterial Composition ◽

Cultivable Bacteria

Acquarossa river (Viterbo, Italy) was the site of a prospering Etruscan civilization thanks to metallurgical activity around 625–550 B.C. This caused the spread of heavy metals throughout the area. Rocks along the river probably act as a filter for these elements and they are covered by two different biofilms (epilithons). They differ for both color and bacterial composition. One is red and is enriched with Pseudomonas strains, while the other one is black and Acinetobacter is the most represented genus. Along the river lay the Infernaccio waterfalls, whose surrounding rocks are covered only by the red epilithon. The bacterial composition of this biofilm was analyzed through high throughput sequencing and compared to those ones of red and black epilithons of Acquarossa river. Moreover, cultivable bacteria were isolated and their phenotype (i.e., resistance against antibiotics and heavy metals) was studied. As previously observed in the case of Acquarossa river, characterization of bacterial composition of the Infernaccio red epilithon revealed that the two most represented genera were Acinetobacter and Pseudomonas. Nonetheless, these strains differed from those isolated from Acquarossa, as revealed by RAPD analysis. This work, besides increasing knowledge about the ecological properties of this site, allowed to isolate new bacterial strains, which could potentially be exploited for biotechnological applications, because of their resistance against environmental pollutants.

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Variations in gut bacterial communities of hooded crane (Grus monacha) over spatial-temporal scales

PeerJ ◽

10.7717/peerj.7045 ◽

2019 ◽

Vol 7 ◽

pp. e7045 ◽

Cited By ~ 6

Author(s):

Yuanqiu Dong ◽

Xingjia Xiang ◽

Guanghong Zhao ◽

Yunwei Song ◽

Lizhi Zhou

Keyword(s):

Bacterial Community ◽

Bacterial Communities ◽

Seasonal Changes ◽

High Throughput Sequencing ◽

Bacterial Composition ◽

Gut Microbe ◽

Host Life ◽

Internal And External Factors ◽

Gut Microbial Community ◽

Grus Monacha

BackgroundMicrobes have been recognized as important symbionts to regulate host life. The animal gut harbors abundance and diverse bacteria. Numerous internal and external factors influence intestinal bacterial communities, including diet, seasonal fluctuations and habitat sites. However, the factors that influence the gut bacterial communities of wild bird is poorly characterized.MethodsBy high-throughput sequencing and statistical analysis, we investigated the variations in gut bacterial communities of the hooded cranes at three wintering stages in Caizi (CZL) and Shengjin Lake (SJL), which are two shallow lakes in the middle and lower Yangtze River floodplain.ResultsOur results revealed significant differences in gut bacterial community structure and diversity among different sampling sites and wintering stages. Seasonal changes have a significant impact on the gut microbe composition of hooded cranes in the two lakes. ANOSIM analysis demonstrated that the samples in CZL had greater differences in the gut bacterial composition than that in SJL. Our data showed strong evidence that the host’s gut filtering might be an important factor in shaping bacterial community according to mean nearest taxon distance (MNTD). The PICRUSt analysis showed that the predicted metagenomes associated with the gut microbiome were carbohydrate metabolism, amino acid metabolism and energy metabolism over the entire wintering period at the two lakes.ConclusionsThe results demonstrated that both seasonal changes and habitat sites have significant impact on the gut bacterial communities of hooded cranes. In addition, predictive function of gut microbes in hooded cranes varied over time. These results provide new insights into the gut microbial community of the cranes, which serves as a foundation for future studies.

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