Synthetic biology tools to engineer microbial communities for biotechnology

NS McCarty, R Ledesma-Amaro - Trends in biotechnology, 2019 - cell.com
Microbial consortia have been used in biotechnology processes, including fermentation,
waste treatment, and agriculture, for millennia. Today, synthetic biologists are increasingly …

[HTML][HTML] Network analysis methods for studying microbial communities: A mini review

MS Matchado, M Lauber, S Reitmeier… - Computational and …, 2021 - Elsevier
Microorganisms including bacteria, fungi, viruses, protists and archaea live as communities
in complex and contiguous environments. They engage in numerous inter-and intra …

Co‐occurrence is not evidence of ecological interactions

FG Blanchet, K Cazelles, D Gravel - Ecology Letters, 2020 - Wiley Online Library
There is a rich amount of information in co‐occurrence (presence–absence) data that could
be used to understand community assembly. This proposition first envisioned by Forbes …

Microbiome multi-omics network analysis: statistical considerations, limitations, and opportunities

D Jiang, CR Armour, C Hu, M Mei, C Tian… - Frontiers in …, 2019 - frontiersin.org
The advent of large-scale microbiome studies affords newfound analytical opportunities to
understand how these communities of microbes operate and relate to their environment …

'NetShift': a methodology for understanding 'driver microbes' from healthy and disease microbiome datasets

BK Kuntal, P Chandrakar, S Sadhu… - The ISME journal, 2019 - academic.oup.com
The combined effect of mutual association within the co-inhabiting microbes in human body
is known to play a major role in determining health status of individuals. The differential …

Endophytic bacterial communities associated with roots and leaves of plants growing in Chilean extreme environments

Q Zhang, JJ Acuña, NG Inostroza, ML Mora, S Radic… - Scientific reports, 2019 - nature.com
Several studies have demonstrated the relevance of endophytic bacteria on the growth and
fitness of agriculturally-relevant plants. To our knowledge, however, little information is …

Current methods, common practices, and perspectives in tracking and monitoring bioinoculants in soil

A Manfredini, E Malusà, C Costa, F Pallottino… - Frontiers in …, 2021 - frontiersin.org
Microorganisms promised to lead the bio-based revolution for a more sustainable
agriculture. Beneficial microorganisms could be a valid alternative to the use of chemical …

Fungal endophytic community and diversity associated with desert shrubs driven by plant identity and organ differentiation in extremely arid desert ecosystem

Y Zuo, X Li, J Yang, J Liu, L Zhao, X He - Journal of Fungi, 2021 - mdpi.com
Despite desert ecosystem being crucial to our understanding of natural geography, species
evolution and global climate change, there is limited information on the dynamics of their …

Metagenomics insights into the microbial diversity and microbiome network analysis on the heterogeneity of influent to effluent water

B Azli, MN Razak, AR Omar, NA Mohd Zain… - Frontiers in …, 2022 - frontiersin.org
Sanitizing the water sources of local communities is important to control the spread of
microbial resistance genes, especially those for water-borne illnesses. The activities of …

Structure and co-occurrence patterns of bacterial communities associated with white faeces disease outbreaks in Pacific white-leg shrimp Penaeus vannamei …

YR Alfiansah, S Peters, J Harder, C Hassenrück… - Scientific reports, 2020 - nature.com
Bacterial diseases cause production failures in shrimp aquacultures. To understand
environmental conditions and bacterial community dynamics contributing to white faeces …