Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

O'Dea, Christian; Huerlimann, Roger; Masters, Nicole; Kuballa, Anna; Veal, Cameron; Fisher, Paul; Stratton, Helen; Katouli, Mohammad

doi:10.3390/microorganisms9081721

Cited by 4 publications

(2 citation statements)

References 63 publications

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“…This view is also supported by findings that show that 16S rRNA regions have different advantages for identifying distinct microbes, largely depending on their taxonomy. For example, the V1–V2 region can be used to accurately identify a large number of clinically important strains [ 44 , 45 ], whereas the V1–V3 variable region can reveal a large number of endemic microbial groups [ 46 ]. However, it is worth pointing out that the primers used for the full-length 16S rRNA amplification and PacBio sequencing (27F/1492R) fail to fully cover the conserved regions of archaea, whose identification often rely on the 23F/1492R primer pair [ 47 , 48 ], and this also contributes to sequencing technique-generated taxonomic differences.…”

Section: Discussionmentioning

confidence: 99%

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Wang

Cui

et al. 2022

Genes

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Marine biofilms are a collective of microbes that can grow on many different surfaces immersed in marine environments. Estimating the microbial richness and specificity of a marine biofilm community is a challenging task due to the high complexity in comparison with seawater. Here, we compared the resolution of full-length 16S rRNA gene sequencing technique of a PacBio platform for microbe identification in marine biofilms with the results of partial 16S rRNA gene sequencing of traditional Illumina PE250 platform. At the same time, the microbial richness, diversity, and composition of adjacent seawater communities in the same batch of samples were analyzed. Both techniques revealed higher species richness, as reflected by the Chao1 index, in the biofilms than that in the seawater communities. Moreover, compared with Illumina sequencing, PacBio sequencing detected more specific species for biofilms and less specific species for seawater. Members of Vibrio, Arcobacter, Photobacterium, Pseudoalteromonas, and Thalassomonas were significantly enriched in the biofilms, which is consistent with the previous understanding of species adapted to a surface-associated lifestyle and validates the taxonomic analyses in the current study. To conclude, the full-length sequencing of 16S rRNA genes has probably a stronger ability to analyze more complex microbial communities, such as marine biofilms, the species richness of which has probably been under-estimated in previous studies.

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Section: Discussionmentioning

confidence: 99%

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Wang

Cui

et al. 2022

Genes

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“…Microbial diversity analysis has demonstrated its significance as science and technology has progressed. For example, the process can indicate changes in microbial populations in soils, intestines, plants, and other ecosystems (Steinrucken et al 2016;Niu et al 2017;O'Dea et al 2021;Wang et al 2021b;Xi et al 2021).…”

Section: Introductionmentioning

confidence: 99%

Effect of powdery mildew on interleaf microbial communities and leaf antioxidant enzyme systems

Wang

Jiang

2023

J. For. Res.

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Chinese peony (Paeonia lactiflora Pall.) is both medicinally and aesthetically beneficial. Powdery mildew is a common fungal disease that seriously jeopardizes the value of numerous species, including peonies as a crop. In order to provide a basis for the prevention and treatment of peony powdery mildew, we examined the microbial diversity, the malondialdehyde (MDA) concentrations and antioxidant enzyme activities of peony leaves infected with three levels of powdery mildew to determine any modifications to the leaf's antioxidant enzyme systems and microbial community structure following the onset of disease. The results show that the MDA content rose as the degree of infection became worse. Antioxidant enzyme activity rose and then declined. Following the initiation of powdery mildew, fungal community diversity decreased, whereas there was not any appreciable change in bacterial communities according to microbial diversity sequencing. The relative abundance of more than half of fungal species decreased, with the bacterial genera displaying both abundant and diminished communities with less pronounced alterations in their community structure after the disease spread. Significant different taxa that were critical to the organization of each microbiome were found. Correlation analysis showed that the relative abundance of powdery mildew pathogenic fungal genus Erysiphe was correlated with those of 11 fungal genera and one bacterial genus. Among them, Aureobasidium, Neosetophoma and Sclerostagonospora showed significant positive correlations with Erysiphe and MDA.

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Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

Stefanini,

Karekar,

Ale Enriquez

et al. 2024

Microbiol Spectr

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We examined the microbial populations present in fecal samples of macropods capable of utilizing a mixture of hydrogen and carbon dioxide (70:30) percent. The feces samples were cultured under anaerobic conditions, and production of methane or acetic acids characteristic for methanogenesis and homoacetogenesis was measured. While the feces of adult macropods mainly produced methane from the substrate, the sample from a 2-month-old juvenile kangaroo only produced acetic acid and no methane. The stable highly enriched culture of the joey kangaroo was sequenced to examine the V3 and V4 regions of the 16S rRNA gene. The results showed that over 70% of gene copies belonged to the Clostridia class, with Paraclostridium and Blautia as the most predominant genera. The culture further showed the presence of Actinomyces spp., a genus which has only been identified in the GI tract of macropods in a few studies, and where none, to our knowledge, have been classified as homoacetogenic. The joey kangaroo mixed culture showed a doubling time of 3.54 h and a specific growth rate of 0.199/h, faster than what has been observed for homoacetogenic bacteria in general. IMPORTANCE Enteric methane emissions from cattle are a significant contributor to greenhouse gas emissions worldwide. Methane emissions not only contribute to climate change but also represent a loss of energy from the animal's diet. However, methanogens play an important role as hydrogen sink to rumen systems; without it, the performance of hydrolytic organisms diminishes. Therefore, effective strategies of methanogen inhibition would be enhanced in conjunction with the addition of alternative hydrogen sinks to the rumen. The significance of our research is to identify homoacetogens present in the GI tract of kangaroos and to present their performance in vitro , demonstrating their capability to serve as alternatives to rumen methanogens.

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Microbial Diversity Profiling of Gut Microbiota of Macropus giganteus Using Three Hypervariable Regions of the Bacterial 16S rRNA

Cited by 4 publications

References 63 publications

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Microbial Richness of Marine Biofilms Revealed by Sequencing Full-Length 16S rRNA Genes

Effect of powdery mildew on interleaf microbial communities and leaf antioxidant enzyme systems

Examining homoacetogens in feces from adult and juvenile kangaroos with the aim of finding competitive strains to hydrogenotrophic methanogens

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