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Life
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Interactions between Microorganisms, Their Environment and Host
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Interactions between Microorganisms, Their Environment and Host

A special issue of Life (ISSN 2075-1729). This special issue belongs to the section "Microbiology".

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 10043

Special Issue Editors

Dr. Manish Kumar

E-Mail Website
Guest Editor
Department of Pediatrics, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0760, USA
Interests: systems biology; microbial communities; computational biology; mathematical modeling; biofuel production
Special Issues, Collections and Topics in MDPI journals
Dr. Partho Sen

E-Mail Website
Guest Editor
Turku Bioscience Centre, University of Turku, FI-20520 Turku, Finland
Interests: microbiome; computational biology; systems biology; bioinformatics; metabolomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Organisms do not live alone in nature. They are inhabited by trillions of microorganisms such as archaea, bacteria, fungi, and viruses, collectively known as the microbiota. Recent research efforts suggest that the associated microbiota plays a crucial role in the health and development of the host, including humans and plants. For example, several diseases, such as cancer, inflammatory bowel disease, obesity, cardiovascular disease, colon cancer, and autoimmune disorders, are found to be strongly associated with human microbiota dysbiosis. Similarly, plant-associated microbiota play advantageous roles in stress tolerance and resistance to pathogens, nutrient uptake, and growth promotion.

With the help of current approaches, such as metagenomics (16S ribosomal (r)RNA amplicon and shotgun sequencing), as well as mass spectrometry-based analyses (metaproteomic and metabolomics analyses), metatranscriptomics, microfluidics, bioreactors, culturomics,  and imaging technologies, we have started to understand the different microbiota and their interactions with the host. Moreover, various computational approaches, such as kinetics and constraint-based modeling, are also being employed to complement experimental approaches in exploring these complex interactions. With evidence mounting of the different microbiota's benefits to the host, researchers are focusing on engineering the microbiota to enhance the health and development of the host and prevent the associated diseases. However, despite current advancements in understanding environment-dependent microorganism–microorganism and host–microorganism interactions, much more research still needs to be conducted.

This Special Issue of Life aims to showcase advancements in the study of the interactions among the host, the associated microbiota, and the environment. For this purpose, we invite the submission of research articles, review articles, and short communications that cover any aspect of the metagenomic and metatranscriptomic analyses of microbiomes (for example, human and plant/soil microbiomes), mass spectrometry-based analyses of microbiota, an understanding of microorganism–microorganism and host–microorganism interactions, the influence of diets/nutrients on these interactions, computational approaches to understand the interaction, and microbiota/microbiome engineering at the individual species level or as an ecosystem. 

Dr. Manish Kumar
Dr. Partho Sen
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Life is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • microbiome
  • microbiota
  • microorganism–microorganism interactions
  • host–microorganism interactions
  • metagenomics
  • metatranscriptomics
  • metaproteomics
  • metabolomics
  • microbiota engineering
  • modeling microbial communities

Published Papers (5 papers)

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18 pages, 3284 KiB  
Article
Increased Trypanosoma cruzi Growth during Infection of Macrophages Cultured on Collagen I Matrix
by Jorgete Logullo, Israel Diniz-Lima, Juliana Dutra B. Rocha, Suzana Cortê-Real, Elias Barbosa da Silva-Júnior, Joyce Cristina Guimarães-de-Oliveira, Alexandre Morrot, Leonardo Marques da Fonseca, Leonardo Freire-de-Lima, Debora Decote-Ricardo and Celio Geraldo Freire-de-Lima
Life 2023, 13(4), 1063; https://doi.org/10.3390/life13041063 - 21 Apr 2023
Viewed by 1453
Abstract
The interactions between cell and cellular matrix confers plasticity to each body tissue, influencing the cellular migratory capacity. Macrophages rely on motility to promote their physiological function. These phagocytes are determinant for the control of invasive infections, and their immunological role largely depends [...] Read more.
The interactions between cell and cellular matrix confers plasticity to each body tissue, influencing the cellular migratory capacity. Macrophages rely on motility to promote their physiological function. These phagocytes are determinant for the control of invasive infections, and their immunological role largely depends on their ability to migrate and adhere to tissue. Therefore, they interact with the components of the extracellular matrix through their adhesion receptors, conferring morphological modifications that change their shape during migration. Nevertheless, the need to use in vitro cell growth models with the conditioning of three-dimensional synthetic matrices to mimic the dynamics of cell-matrix interaction has been increasingly studied. This becomes more important to effectively understand the changes occurring in phagocyte morphology in the context of infection progression, such as in Chagas disease. This disease is caused by the intracellular pathogen Trypanosoma cruzi, capable of infecting macrophages, determinant cells in the anti-trypanosomatid immunity. In the present study, we sought to understand how an in vitro extracellular matrix model interferes with T. cruzi infection in macrophages. Using different time intervals and parasite ratios, we evaluated the cell morphology and parasite replication rate in the presence of 3D collagen I matrix. Nevertheless, microscopy techniques such as scanning electron microscopy were crucial to trace macrophage-matrix interactions. In the present work, we demonstrated for the first time that the macrophage-matrix interaction favors T. cruzi in vitro replication and the release of anti-inflammatory cytokines during macrophage infection, in addition to drastically altering the morphology of the macrophages and promoting the formation of migratory macrophages. Full article
(This article belongs to the Special Issue Interactions between Microorganisms, Their Environment and Host)
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10 pages, 1332 KiB  
Article
Molecular Identification of Protozoan Sarcocystis in Different Types of Water Bodies in Lithuania
by Agnė Baranauskaitė, Živilė Strazdaitė-Žielienė, Elena Servienė, Dalius Butkauskas and Petras Prakas
Life 2023, 13(1), 51; https://doi.org/10.3390/life13010051 - 24 Dec 2022
Cited by 2 | Viewed by 1361
Abstract
Representatives of the genus Sarcocystis are unicellular parasites having a two-host life cycle and infecting mammals, birds, and reptiles. Until now, Sarcocystis spp. have been mainly investigated in definitive and intermediate hosts. Only a few studies have been conducted on the detection of [...] Read more.
Representatives of the genus Sarcocystis are unicellular parasites having a two-host life cycle and infecting mammals, birds, and reptiles. Until now, Sarcocystis spp. have been mainly investigated in definitive and intermediate hosts. Only a few studies have been conducted on the detection of Sarcocystis parasites in water samples. The aim of this research was to examine whether the prevalence of Sarcocystis spp. parasitizing farm animals varies in different types of water bodies. Water samples (n = 150) were collected from the entire territory of Lithuania, dividing water bodies into five groups (lakes, rivers, ponds/canals, swamps, and the inshore zone of the territorial Baltic Sea area). One-liter samples were filtered and subsequently analyzed using nested PCR. At least one of the analyzed Sarcocystis spp. (S. arieticanis, S. bertrami, S. bovifelis, S. capracanis, S. cruzi, S. hirsuta, S. miescheriana, and S. tenella) was determined in all examined samples from water bodies. No significant difference in Sarcocystis spp. prevalence between different types of water sources was detected. Our research proved that selecting appropriate primers is important for the accurate identification of parasites in samples collected from water bodies. Full article
(This article belongs to the Special Issue Interactions between Microorganisms, Their Environment and Host)
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15 pages, 3379 KiB  
Article
Bacterial and Fungal Co-Occurrence in the Nudibranch, Pteraeolidia semperi
by Ming Sheng Ng, Nathaniel Soon, Ying Chang and Benjamin J. Wainwright
Life 2022, 12(12), 1988; https://doi.org/10.3390/life12121988 - 28 Nov 2022
Cited by 1 | Viewed by 2047
Abstract
Despite the increasing recognition and importance surrounding bacterial and fungal interactions, and their critical contributions to ecosystem functioning and host fitness, studies examining their co-occurrence remain in their infancy. Similarly, studies have yet to characterise the bacterial and fungal communities associated with nudibranchs [...] Read more.
Despite the increasing recognition and importance surrounding bacterial and fungal interactions, and their critical contributions to ecosystem functioning and host fitness, studies examining their co-occurrence remain in their infancy. Similarly, studies have yet to characterise the bacterial and fungal communities associated with nudibranchs or their core microbial members. Doing this can advance our understanding of how the microbiome helps a host adapt and persist in its environment. In this study, we characterised the bacterial and fungal communities associated with 46 Pteraeolidia semperi nudibranch individuals collected from four offshore islands in Singapore. We found no distinct spatial structuring of microbial community, richness, or diversity across sampling locations. The bacterial genera Mycoplasma and Endozoicomonas were found across all samples and islands. The fungal genus Leucoagaricus was found with the highest occurrence, but was not found everywhere, and this is the first record of its reported presence in marine environments. The co-occurrence network suggests that bacterial and fungal interactions are limited, but we identified the bacterial family Colwelliaceae as a potential keystone taxon with its disproportionately high number of edges. Furthermore, Colwelliaceae clusters together with other bacterial families such as Pseudoalteromonadaceae and Alteromonadaceae, all of which have possible roles in the digestion of food. Full article
(This article belongs to the Special Issue Interactions between Microorganisms, Their Environment and Host)
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26 pages, 6994 KiB  
Article
Stochastic Inoculum, Biotic Filtering and Species-Specific Seed Transmission Shape the Rare Microbiome of Plants
by David Johnston-Monje, Janneth P. Gutiérrez and Luis Augusto Becerra Lopez-Lavalle
Life 2022, 12(9), 1372; https://doi.org/10.3390/life12091372 - 02 Sep 2022
Cited by 5 | Viewed by 2450
Abstract
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and [...] Read more.
A plant’s health and productivity is influenced by its associated microbes. Although the common/core microbiome is often thought to be the most influential, significant numbers of rare or uncommon microbes (e.g., specialized endosymbionts) may also play an important role in the health and productivity of certain plants in certain environments. To help identify rare/specialized bacteria and fungi in the most important angiosperm plants, we contrasted microbiomes of the seeds, spermospheres, shoots, roots and rhizospheres of Arabidopsis, Brachypodium, maize, wheat, sugarcane, rice, tomato, coffee, common bean, cassava, soybean, switchgrass, sunflower, Brachiaria, barley, sorghum and pea. Plants were grown inside sealed jars on sterile sand or farm soil. Seeds and spermospheres contained some uncommon bacteria and many fungi, suggesting at least some of the rare microbiome is vertically transmitted. About 95% and 86% of fungal and bacterial diversity inside plants was uncommon; however, judging by read abundance, uncommon fungal cells are about half of the mycobiome, while uncommon bacterial cells make up less than 11% of the microbiome. Uncommon-seed-transmitted microbiomes consisted mostly of Proteobacteria, Firmicutes, Bacteriodetes, Ascomycetes and Basidiomycetes, which most heavily colonized shoots, to a lesser extent roots, and least of all, rhizospheres. Soil served as a more diverse source of rare microbes than seeds, replacing or excluding the majority of the uncommon-seed-transmitted microbiome. With the rarest microbes, their colonization pattern could either be the result of stringent biotic filtering by most plants, or uneven/stochastic inoculum distribution in seeds or soil. Several strong plant–microbe associations were observed, such as seed transmission to shoots, roots and/or rhizospheres of Sarocladium zeae (maize), Penicillium (pea and Phaseolus), and Curvularia (sugarcane), while robust bacterial colonization from cassava field soil occurred with the cyanobacteria Leptolyngbya into Arabidopsis and Panicum roots, and Streptomyces into cassava roots. Some abundant microbes such as Sakaguchia in rice shoots or Vermispora in Arabidopsis roots appeared in no other samples, suggesting that they were infrequent, stochastically deposited propagules from either soil or seed (impossible to know based on the available data). Future experiments with culturing and cross-inoculation of these microbes between plants may help us better understand host preferences and their role in plant productivity, perhaps leading to their use in crop microbiome engineering and enhancement of agricultural production. Full article
(This article belongs to the Special Issue Interactions between Microorganisms, Their Environment and Host)
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9 pages, 1517 KiB  
Case Report
Microbiota of the Colonic Diverticula in the Complicated Form of Diverticulitis: A Case Report
by Dina Yarullina, Yuliia Pankratova, Olga Karaseva, Tatiana Grigoryeva and Oleg Karpukhin
Life 2022, 12(12), 2129; https://doi.org/10.3390/life12122129 - 16 Dec 2022
Viewed by 1555
Abstract
Intestinal microbiota appears to be implicated in the pathogenesis of diverticular disease. We present the case of a patient with diverticular colon disease complicated by a pelvic abscess. During the successful surgical treatment, two specimens were taken from the resected colon segment for [...] Read more.
Intestinal microbiota appears to be implicated in the pathogenesis of diverticular disease. We present the case of a patient with diverticular colon disease complicated by a pelvic abscess. During the successful surgical treatment, two specimens were taken from the resected colon segment for the microbiota analysis: an inflamed and perforated diverticulum and a diverticulum without signs of inflammation. Culturing and 16S rRNA gene sequencing revealed significant changes in the microbial community structure and composition associated with the acute inflammation and perforation of the colonic diverticulum. The characteristics that are usually associated with the inflammatory process in the gut, namely reduced microbial diversity and richness, decreased Firmicutes-to-Bacteroidetes (F/B) ratio, depletion of butyrate-producing bacteria, and Enterobacteriaceae blooming, were more pronounced in the non-inflamed diverticulum rather than in the adjacent inflamed and perforated one. This is the first study of the intraluminal microbiota of the diverticular pockets, which is more relevant to the etiology of diverticular disease than mucosa-associated microbiota via biopsies and luminal microbiota via fecal samples. Full article
(This article belongs to the Special Issue Interactions between Microorganisms, Their Environment and Host)
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