Bacterial species rarely work together

Palmer, Jacob D; Foster, Kevin

doi:10.1126/science.abn5093

Cited by 174 publications

(136 citation statements)

References 16 publications

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“…Based on this hypothesis, positive interactions between different members of microbial species should be expected to occur in the higher range under stressful environments than in optimum conditions where competitions gain more importance. This hypothesis has been proven in several recent studies ( Piccardi et al, 2019 ; Palmer and Foster, 2022 ) but has not been tested for microbes under different agricultural management in the face of multiple stress factors. Therefore, one promising approach is to expose plants to complex soil microbes originating from areas with historical stress conditions.…”

Section: The Application Of (Complex) Microbiome-based Approaches Tow...mentioning

confidence: 99%

Conventional vs. Organic Agriculture–Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

Azarbad

2022

Front. Microbiol.

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In recent years, agricultural productivity has been affected dramatically by climate-related events such as drought. On the other hand, agricultural intensification is expected to increase to satisfy the need for increased global food production. Microbes associated with soil and plants produce a range of bioactive natural products that significantly contribute to crop stress tolerance. Therefore, a better understanding of the parallel effects of agricultural management (conventional and organic croplands) and climate conditions on soil-microbe-plant interactions is crucial to maximizing the effort in engineering a plant microbiome that can better support productivity in agroecosystems. This paper provides a general overview of the major current debates on conventional and organic farming performance regarding yields, particularly under ambient and future climate conditions. With the main focus on cropland, the effect of agricultural management on soil and plant microbiomes is discussed. In addition, the advantage of incorporating microbiome-based approaches into current farming practices to ensure agricultural productivity with less adverse environmental impacts is highlighted. To enhance crop production under organic farming without massive land-use changes and expansion of farmland, the microbial-based approach can be used to ensure higher productivity, particularly under a rapidly changing climate.

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Section: The Application Of (Complex) Microbiome-based Approaches Tow...mentioning

confidence: 99%

Conventional vs. Organic Agriculture–Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

Azarbad

2022

Front. Microbiol.

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“…Surprisingly, we found that the most universal bacterial pairs are almost always positively (as opposed to negatively) correlated. Positive bacterial interactions have been the subject of recent controversy [9,15,49]. Ecological theory predicts that strong positive interactions should be rare in natural communities because species interdependencies can hamper community assembly and stability [14,17].…”

Section: Discussionmentioning

confidence: 99%

“…Knowing the overall direction and strength of these correlative relationships is important, not only because they partly reflect the ecological relationships that mediate gut microbial processes, but also because overall correlation patterns can affect gut microbiome assembly, stability, and productivity [14, 15]. For instance, sets of microbes that exhibit strong, positive relationships within hosts sometimes represent networks of cooperating taxa that promote each other’s growth [5, 9, 16].…”

Section: Introductionmentioning

confidence: 99%

Universal gut microbial relationships in the gut microbiome of wild baboons

Roche

Björk

Dasari

et al. 2022

Preprint

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Ecological relationships between bacteria mediate the services that gut microbiomes provide to their hosts. Knowing the overall direction and strength of these relationships within hosts, and their generalizability across hosts, is essential to learn how microbial ecology scales up to affect microbiome assembly, dynamics, and host health. Here we gain insight into these patterns by inferring thousands of correlations in bacterial abundance between pairs of gut microbiome taxa from extensive time series data, consisting of 5,534 microbiome profiles from 56 wild baboon hosts over a 13-year period. We model these time series using a statistically robust, multinomial logistic-normal modeling framework and test the degree to which bacterial abundance correlations are consistent across hosts (i.e., "univeral") or individualized to each host. We also compare these patterns to two publicly available human data sets. We find that baboon gut microbial relationships are largely universal: correlation patterns within each baboon host reflect a mixture of idiosyncratic and shared patterns, but the shared pattern dominates by almost 2-fold. Surprisingly, the strongest and most consistently correlated bacterial pairs across hosts were overwhelmingly positively correlated and typically belonged to the same family - a 3-fold enrichment compared to pairs drawn from the data set as a whole. The bias towards universal, positive bacterial correlations was also apparent in monthly samples from human infants, and bacterial families that had universal relationships in baboons also tended to be universal in human infants. Together, our results advance our understanding of the relationships that shape gut microbial ecosystems, with implications for microbiome personalization, community assembly and stability, and the feasibility of microbiome interventions to improve host health.

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“…It has only recently become apparent how important social interactions are to microbial ecology and evolution 68,69 . Antagonistic interactions appear to be more common than cooperation or commensalism 1 , at least for species that are capable of being cultured. The Type VI secretion system - a ballistic harpoon containing multiple types of toxins capable of quickly killing susceptible cells, represents the cutting-edge of microbial weaponry.…”

Section: Discussionmentioning

confidence: 99%

Trade-offs constrain adaptive pathways to T6 survival

MacGillivray

Wiesenfeld

et al. 2022

Preprint

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Many microbial communities are characterized by intense competition for nutrients and space. One way for an organism to gain control of these resources is by eliminating nearby competitors. The Type VI Secretion System (T6) is a nano-harpoon used by many bacteria to inject toxins into neighboring cells. While much is understood about mechanisms of T6-mediated toxicity, little is known about the ways that competitors can defend themselves against this attack, especially in the absence of their own T6. Here we use directed evolution to examine the evolution of T6 resistance, subjecting eight replicate populations of Escherichia coli to T6 attack by Vibrio cholerae. Over ~500 generations of competition, the E. coli evolved to survive T6 attack an average of 27-fold better than their ancestor. Whole genome sequencing reveals extensive parallel evolution. In fact, we found only two pathways to increased T6 survival: apaH was mutated in six of the eight replicate populations, while the other two populations each had mutations in both yejM and yjeP. Synthetic reconstruction of individual and combined mutations demonstrate that yejM and yjeP are synergistic, with yejM requiring the mutation in yejP to provide a benefit. However, the mutations we identified are pleiotropic, reducing cellular growth rates, and increasing susceptibility to antibiotics and elevated pH. These trade-offs underlie the effectiveness of T6 as a bacterial weapon, and help us understand how the T6 shapes the evolution of bacterial interactions.

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Bacterial species rarely work together

Abstract: Competition is prevalent and could be harnessed as an alternative to antibiotics

Cited by 174 publications

References 16 publications

Conventional vs. Organic Agriculture–Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

Conventional vs. Organic Agriculture–Which One Promotes Better Yields and Microbial Resilience in Rapidly Changing Climates?

Universal gut microbial relationships in the gut microbiome of wild baboons

Trade-offs constrain adaptive pathways to T6 survival

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